Variant report

Variant	rs9979962
Chromosome Location	chr21:47968307-47968308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	BRCA1	chr21:47968213-47968319	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr21:47961062..47963795-chr21:47966527..47968756,2	MCF-7	breast:
2	chr21:47966998..47969983-chr21:47970602..47975589,5	MCF-7	breast:
3	chr17:59415209..59417169-chr21:47966964..47969396,2	MCF-7	breast:
4	chr21:47967795..47973717-chr21:47974569..47979109,7	K562	blood:

Variant related genes	Relation type
DIP2A	TF binding region
ENSG00000160305	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10854482	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs11089076	0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs11701286	0.87[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs11701512	0.94[ASN][1000 genomes]
rs12627695	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs13047696	0.81[JPT][hapmap];0.83[MEX][hapmap]
rs17371795	0.81[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs2016807	0.88[ASN][1000 genomes]
rs2032110	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.86[ASN][1000 genomes]
rs2070429	0.81[JPT][hapmap];0.91[MEX][hapmap]
rs2070431	0.81[JPT][hapmap];0.91[MEX][hapmap]
rs2073378	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2078203	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs2239574	0.81[JPT][hapmap];0.82[MEX][hapmap]
rs2249060	0.80[CHB][hapmap]
rs2330590	0.80[ASN][1000 genomes]
rs2330591	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2330592	0.88[ASN][1000 genomes]
rs2839222	0.80[CHB][hapmap]
rs2839224	0.80[CHB][hapmap]
rs2839232	0.81[CHB][hapmap];0.94[JPT][hapmap]
rs2839235	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs2839251	0.87[CHB][hapmap];0.80[CHD][hapmap];1.00[JPT][hapmap]
rs2839262	0.87[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap]
rs2839267	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2839271	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2839273	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2839274	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2839283	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.86[ASN][1000 genomes]
rs2839289	0.85[ASN][1000 genomes]
rs2839292	0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2839298	0.88[JPT][hapmap]
rs2839305	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs2839321	0.87[JPT][hapmap];0.91[MEX][hapmap]
rs34722617	0.81[JPT][hapmap]
rs4143362	0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4818837	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4818846	0.81[JPT][hapmap]
rs7277463	0.81[ASN][1000 genomes]
rs7279052	0.87[CHB][hapmap];0.86[CHD][hapmap];1.00[JPT][hapmap]
rs7280077	0.80[ASN][1000 genomes]
rs7282126	0.81[JPT][hapmap]
rs7282296	0.93[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs762251	0.93[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs8127280	0.81[JPT][hapmap]
rs8129188	0.86[ASN][1000 genomes]
rs8130538	0.80[ASN][1000 genomes]
rs8132320	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap]
rs8134014	0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.87[ASN][1000 genomes]
rs8134832	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs9306152	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9637222	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9637223	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:33 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1065959	chr21:47188878-48091343	Bivalent Enhancer Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	n/a
2	nsv531580	chr21:47221774-48090317	Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	101 gene(s)	inside rSNPs	n/a
3	nsv918103	chr21:47297067-48089510	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	99 gene(s)	inside rSNPs	n/a
4	nsv470910	chr21:47353775-48084988	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
5	nsv1059118	chr21:47398331-48090457	Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
6	nsv544494	chr21:47398331-48090457	Strong transcription Weak transcription Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
7	nsv934264	chr21:47401083-48090317	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	95 gene(s)	inside rSNPs	n/a
8	nsv948761	chr21:47587940-48069930	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	n/a
9	nsv1055239	chr21:47591378-48090317	Enhancers Strong transcription Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
10	nsv544495	chr21:47591378-48090317	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	85 gene(s)	inside rSNPs	n/a
11	nsv949706	chr21:47625544-48069930	Strong transcription Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
12	nsv529496	chr21:47634193-48090317	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	82 gene(s)	inside rSNPs	n/a
13	nsv933061	chr21:47746204-48031515	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	n/a
14	nsv1062858	chr21:47750884-48091343	Enhancers Genic enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
15	nsv1056321	chr21:47835146-47973412	Strong transcription Genic enhancers Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
16	nsv917208	chr21:47836346-47988603	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
17	nsv1058397	chr21:47851176-48091343	Flanking Active TSS Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
18	nsv459312	chr21:47856106-47985655	Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
19	nsv587998	chr21:47856106-47985655	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
20	nsv1065502	chr21:47865215-48091343	Strong transcription Genic enhancers Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
21	nsv1056152	chr21:47875370-47979259	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	n/a
22	nsv1061442	chr21:47875370-48091343	Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	n/a
23	nsv1059466	chr21:47894705-48096945	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
24	nsv1061185	chr21:47901250-48096945	Enhancers Flanking Active TSS Strong transcription Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	n/a
25	nsv1057566	chr21:47915583-48029698	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	n/a
26	nsv587999	chr21:47941916-48103851	Weak transcription Strong transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
27	nsv1058589	chr21:47948030-48091343	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	n/a
28	nsv1057643	chr21:47953820-48056600	Genic enhancers Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	n/a
29	nsv544497	chr21:47953820-48056600	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	n/a
30	nsv914147	chr21:47958657-47982652	Enhancers Genic enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	n/a
31	nsv459313	chr21:47964259-47982652	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
32	nsv588000	chr21:47964259-47982652	Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a
33	nsv588001	chr21:47966504-47986001	Weak transcription Genic enhancers Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs9979962	S100B	cis	parietal	SCAN
rs9979962	S100B	cis	cerebellum	SCAN
rs9979962	C21orf57	Cis_1M	lymphoblastoid	RTeQTL
rs9979962	PCNT	cis	parietal	SCAN
rs9979962	C21orf57	cis	cerebellum	SCAN
rs9979962	LSS	cis	parietal	SCAN
rs9979962	LSS	cis	cerebellum	SCAN
rs9979962	KRTAP10-3	cis	cerebellum	SCAN
rs9979962	S100B	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47943600-47990600	Strong transcription	Fetal Stomach	stomach
2	chr21:47947200-47975200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr21:47947600-47989000	Strong transcription	Dnd41	blood
4	chr21:47947600-47991000	Strong transcription	Fetal Muscle Leg	muscle
5	chr21:47948000-47968400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr21:47948400-47971600	Strong transcription	Fetal Muscle Trunk	muscle
7	chr21:47948400-47993600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr21:47948600-47971400	Strong transcription	Rectal Mucosa Donor 29	rectum
9	chr21:47948600-47993200	Strong transcription	Fetal Intestine Large	intestine
10	chr21:47948800-47969000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr21:47948800-47970400	Strong transcription	Placenta	Placenta
12	chr21:47948800-47979400	Strong transcription	Liver	Liver
13	chr21:47949000-47969000	Strong transcription	Monocytes-CD14+_RO01746	blood
14	chr21:47949000-47979000	Strong transcription	Adipose Nuclei	Adipose
15	chr21:47949000-47988200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr21:47949000-47993600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr21:47949600-47968600	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr21:47949600-47970200	Strong transcription	Duodenum Mucosa	Duodenum
19	chr21:47949800-47991800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr21:47950000-47968800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr21:47950000-47989200	Strong transcription	Skeletal Muscle Female	skeletal muscle
22	chr21:47950000-47991000	Strong transcription	Sigmoid Colon	Sigmoid Colon
23	chr21:47950200-47993200	Strong transcription	Stomach Smooth Muscle	stomach
24	chr21:47950400-47971800	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr21:47950400-47974400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr21:47952000-47978600	Strong transcription	Skeletal Muscle Male	skeletal muscle
27	chr21:47953000-47974800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:47953000-47988200	Strong transcription	Gastric	stomach
29	chr21:47953000-47988600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:47953200-47968400	Strong transcription	Lung	lung
31	chr21:47953200-47968400	Strong transcription	Spleen	Spleen
32	chr21:47953200-47968600	Strong transcription	Primary B cells from peripheral blood	blood
33	chr21:47953200-47968800	Strong transcription	Placenta Amnion	Placenta Amnion
34	chr21:47953200-47971800	Strong transcription	Thymus	Thymus
35	chr21:47953200-47972000	Strong transcription	Ovary	ovary
36	chr21:47953200-47983400	Strong transcription	Brain Inferior Temporal Lobe	brain
37	chr21:47953200-47988400	Strong transcription	Fetal Intestine Small	intestine
38	chr21:47953200-47993000	Strong transcription	Osteobl	bone
39	chr21:47953400-47969200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr21:47953400-47969200	Strong transcription	HSMMtube	muscle
41	chr21:47953400-47972000	Strong transcription	Brain Angular Gyrus	brain
42	chr21:47953400-47988000	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr21:47953800-47968800	Strong transcription	Brain Cingulate Gyrus	brain
44	chr21:47954200-47969200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr21:47954400-47973000	Strong transcription	HUES48 Cell Line	embryonic stem cell
46	chr21:47955800-47972000	Strong transcription	Rectal Smooth Muscle	rectum
47	chr21:47956000-47978800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr21:47956200-47969200	Strong transcription	Colon Smooth Muscle	Colon
49	chr21:47956200-47969200	Strong transcription	Fetal Thymus	thymus
50	chr21:47956200-48001800	Weak transcription	Stomach Mucosa	stomach

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