Variant report

Variant	rs2839305
Chromosome Location	chr21:47952893-47952894
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:47951124..47955048-chr21:47957159..47961247,5	K562	blood:
2	chr21:47949927..47954811-chr21:47962745..47966393,6	K562	blood:
3	chr21:47951915..47953420-chr21:48055015..48056695,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000160305	Chromatin interaction
ENSG00000160310	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10854482	0.82[CHB][hapmap];0.89[JPT][hapmap]
rs11089074	0.86[ASN][1000 genomes]
rs11089076	0.88[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs11701286	0.82[CHB][hapmap];0.83[JPT][hapmap];0.89[ASN][1000 genomes]
rs11701512	0.90[ASN][1000 genomes]
rs12627695	0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs17371795	0.88[JPT][hapmap]
rs2016807	0.85[ASN][1000 genomes]
rs2032110	0.87[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2073378	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs2078203	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs2330590	0.92[ASN][1000 genomes]
rs2330591	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2330592	0.85[ASN][1000 genomes]
rs2839232	0.82[JPT][hapmap]
rs2839235	0.81[CHB][hapmap];0.82[JPT][hapmap]
rs2839251	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2839262	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs2839267	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs2839271	0.87[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2839273	0.88[CHB][hapmap];0.89[JPT][hapmap];0.80[ASN][1000 genomes]
rs2839274	0.87[CHB][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.81[ASN][1000 genomes]
rs2839283	0.87[CHB][hapmap];0.88[JPT][hapmap];0.83[ASN][1000 genomes]
rs2839289	0.82[ASN][1000 genomes]
rs2839292	0.88[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs2839298	0.88[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2839317	0.83[YRI][hapmap]
rs2839365	0.83[JPT][hapmap]
rs3788266	0.83[JPT][hapmap]
rs4143362	0.88[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4818837	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7275616	0.83[JPT][hapmap]
rs7279052	0.81[CHB][hapmap];0.88[JPT][hapmap]
rs7282296	0.88[CHB][hapmap];0.89[JPT][hapmap]
rs762251	0.88[CHB][hapmap];0.89[JPT][hapmap];0.90[ASN][1000 genomes]
rs8129188	0.83[ASN][1000 genomes]
rs8132320	0.87[CHB][hapmap];0.88[JPT][hapmap]
rs8134014	0.87[CHB][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs8134832	0.89[JPT][hapmap]
rs9306152	0.82[CHB][hapmap];0.83[JPT][hapmap]
rs9637222	0.87[CHB][hapmap];0.93[JPT][hapmap]
rs9637223	0.85[ASN][1000 genomes]
rs9978658	0.82[JPT][hapmap]
rs9979962	0.81[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:28 , 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	nsv869002	chr21:47297268-47963186	Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	n/a
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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
25	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
26	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
27	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
28	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47931800-47953600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr21:47932000-47953400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr21:47932000-47961400	Weak transcription	Fetal Brain Male	brain
4	chr21:47932200-47954000	Weak transcription	A549	lung
5	chr21:47932400-47954400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr21:47932400-47957400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr21:47932600-47953400	Weak transcription	Colonic Mucosa	Colon
8	chr21:47933000-47967200	Weak transcription	Fetal Kidney	kidney
9	chr21:47933600-47953400	Weak transcription	Psoas Muscle	Psoas
10	chr21:47935400-47953400	Weak transcription	NH-A	brain
11	chr21:47935600-47953400	Weak transcription	Brain Anterior Caudate	brain
12	chr21:47937600-47953400	Weak transcription	Brain Angular Gyrus	brain
13	chr21:47937800-47953400	Weak transcription	Brain Hippocampus Middle	brain
14	chr21:47937800-47953400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr21:47938000-47953800	Weak transcription	Brain Cingulate Gyrus	brain
16	chr21:47938000-47955800	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr21:47939400-47953800	Weak transcription	Brain Germinal Matrix	brain
18	chr21:47939600-47953400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr21:47939600-47955600	Weak transcription	Fetal Heart	heart
20	chr21:47943600-47990600	Strong transcription	Fetal Stomach	stomach
21	chr21:47944000-47956800	Weak transcription	K562	blood
22	chr21:47946600-47954600	Weak transcription	Stomach Mucosa	stomach
23	chr21:47947200-47953400	Weak transcription	GM12878-XiMat	blood
24	chr21:47947200-47975200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr21:47947400-47965600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr21:47947600-47967200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr21:47947600-47989000	Strong transcription	Dnd41	blood
28	chr21:47947600-47991000	Strong transcription	Fetal Muscle Leg	muscle
29	chr21:47947800-47953200	Weak transcription	Osteobl	bone
30	chr21:47948000-47953400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr21:47948000-47953400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr21:47948000-47953400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr21:47948000-47953400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr21:47948000-47953400	Weak transcription	Right Ventricle	heart
35	chr21:47948000-47955600	Weak transcription	Right Atrium	heart
36	chr21:47948000-47960200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
37	chr21:47948000-47968400	Strong transcription	Primary monocytes fromperipheralblood	blood
38	chr21:47948200-47953600	Weak transcription	Small Intestine	intestine
39	chr21:47948200-47955400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr21:47948400-47955600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
41	chr21:47948400-47971600	Strong transcription	Fetal Muscle Trunk	muscle
42	chr21:47948400-47993600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr21:47948600-47968000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr21:47948600-47968000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr21:47948600-47971400	Strong transcription	Rectal Mucosa Donor 29	rectum
46	chr21:47948600-47993200	Strong transcription	Fetal Intestine Large	intestine
47	chr21:47948800-47955800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
48	chr21:47948800-47956200	Strong transcription	Primary hematopoietic stem cells	blood
49	chr21:47948800-47969000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr21:47948800-47970400	Strong transcription	Placenta	Placenta

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