Variant report

Variant	rs9976319
Chromosome Location	chr21:47477865-47477866
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:47476412..47478192-chr21:47563693..47565789,2	K562	blood:
2	chr21:47477438..47479279-chr21:47515180..47518074,2	K562	blood:

Variant related genes	Relation type
ENSG00000227438	Chromatin interaction
ENSG00000160282	Chromatin interaction
ENSG00000142173	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:4)

rs_ID	r²[population]
rs12482759	0.96[YRI][hapmap];0.92[AFR][1000 genomes]
rs59359349	0.82[AFR][1000 genomes]
rs915808	1.00[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9974156	0.96[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:26 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1058665	chr21:46719445-47634282	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
2	nsv544486	chr21:46719445-47634282	Bivalent/Poised TSS Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	91 gene(s)	inside rSNPs	diseases
3	nsv1059230	chr21:46956877-47907990	Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
4	nsv544491	chr21:46956877-47907990	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	94 gene(s)	inside rSNPs	n/a
5	nsv1058472	chr21:47027823-47797326	Enhancers Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
6	nsv544492	chr21:47027823-47797326	Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	n/a
7	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
8	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
9	nsv914079	chr21:47243074-47650362	Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	n/a
10	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
11	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
12	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
13	nsv914091	chr21:47383056-47483799	Bivalent Enhancer Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
14	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
15	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
16	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
17	nsv459310	chr21:47409503-47488387	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
18	nsv587935	chr21:47409503-47488387	Enhancers Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	n/a
19	nsv1062861	chr21:47434057-47568806	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
20	nsv531548	chr21:47439416-47516220	Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
21	nsv914097	chr21:47445791-47505084	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
22	nsv914098	chr21:47467894-47619784	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	n/a
23	nsv519834	chr21:47472641-47503311	Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	n/a
24	nsv525728	chr21:47472641-47583506	Enhancers Bivalent/Poised TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	n/a
25	nsv1061087	chr21:47476088-47643219	Enhancers ZNF genes & repeats Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	n/a
26	esv3410971	chr21:47476224-47480822	Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9976319	KRTAP12-2	cis	cerebellum	SCAN
rs9976319	UBE2G2	cis	parietal	SCAN
rs9976319	C21orf84	cis	parietal	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:47468200-47478000	Enhancers	Fetal Muscle Leg	muscle
2	chr21:47470400-47478800	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr21:47471000-47478600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr21:47474600-47480400	Weak transcription	Aorta	Aorta
5	chr21:47476200-47478000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr21:47476200-47478000	Enhancers	Fetal Stomach	stomach
7	chr21:47476400-47478000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr21:47476400-47478400	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
9	chr21:47476400-47478600	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
10	chr21:47476600-47478000	Bivalent Enhancer	Primary T helper cells PMA-I stimulated	--
11	chr21:47476600-47479000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr21:47476800-47478000	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
13	chr21:47476800-47478000	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
14	chr21:47477000-47478200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:47477000-47478400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:47477200-47478000	Bivalent Enhancer	Primary T helper 17 cells PMA-I stimulated	--
17	chr21:47477200-47478200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
18	chr21:47477200-47478800	Bivalent Enhancer	Dnd41	blood
19	chr21:47477200-47479800	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr21:47477200-47480000	Weak transcription	HSMM	muscle
21	chr21:47477200-47480000	Weak transcription	NH-A	brain
22	chr21:47477200-47480200	Weak transcription	Stomach Mucosa	stomach
23	chr21:47477200-47480200	Weak transcription	HSMMtube	muscle
24	chr21:47477400-47478200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr21:47477400-47478200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr21:47477400-47478400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr21:47477400-47479000	Enhancers	Fetal Thymus	thymus
28	chr21:47477400-47479800	Weak transcription	Right Atrium	heart
29	chr21:47477400-47479800	Weak transcription	Osteobl	bone
30	chr21:47477400-47480000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr21:47477400-47480000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr21:47477400-47480000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr21:47477400-47480000	Weak transcription	Adipose Nuclei	Adipose
34	chr21:47477400-47480000	Weak transcription	NHLF	lung
35	chr21:47477400-47480200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr21:47477600-47478000	Flanking Active TSS	Primary T cells from cord blood	blood
37	chr21:47477600-47478000	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr21:47477600-47478600	Weak transcription	Right Ventricle	heart
39	chr21:47477600-47479600	Weak transcription	Spleen	Spleen
40	chr21:47477600-47480000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
41	chr21:47477600-47480000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr21:47477600-47480400	Weak transcription	Ovary	ovary
43	chr21:47477800-47478000	Enhancers	Thymus	Thymus
44	chr21:47477800-47478200	Enhancers	Stomach Smooth Muscle	stomach
45	chr21:47477800-47478800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr21:47477800-47479400	Weak transcription	NHDF-Ad	bronchial
47	chr21:47477800-47479800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr21:47477800-47479800	Weak transcription	Colonic Mucosa	Colon
49	chr21:47477800-47480000	Weak transcription	Rectal Smooth Muscle	rectum
50	chr21:47477800-47480200	Weak transcription	Colon Smooth Muscle	Colon

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