Variant report

Variant	rs10863961
Chromosome Location	chr1:212467847-212467848
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:212458786..212460373-chr1:212467150..212468979,2	MCF-7	breast:
2	chr1:212467247..212471909-chr1:212472711..212476183,6	K562	blood:
3	chr1:212464978..212469431-chr1:212471345..212474474,8	K562	blood:

Variant related genes	Relation type
ENSG00000066027	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10863960	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10863963	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11119899	0.90[ASN][1000 genomes]
rs11119919	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11119920	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs11119924	1.00[CEU][hapmap];0.89[CHB][hapmap];0.82[JPT][hapmap];0.86[EUR][1000 genomes]
rs11119930	0.89[CHB][hapmap]
rs11576437	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11576769	0.88[EUR][1000 genomes]
rs11580285	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11584189	0.86[EUR][1000 genomes]
rs11585215	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11587555	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs11588867	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11589817	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11590242	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs11590672	1.00[CEU][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs12060029	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs12064553	0.85[EUR][1000 genomes]
rs12066356	0.86[ASN][1000 genomes]
rs12096035	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12722832	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12726409	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12727947	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12728266	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12730098	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12734895	0.95[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12736502	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs12737825	0.86[EUR][1000 genomes]
rs12743785	1.00[CEU][hapmap];0.84[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12745269	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12747025	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12756678	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1342151	0.92[YRI][hapmap]
rs1470390	1.00[CEU][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs1493600	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1530451	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17721302	0.95[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2120770	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs2218450	0.92[YRI][hapmap]
rs2297306	0.82[CHB][hapmap]
rs2358448	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2358454	0.88[CEU][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2884465	0.83[EUR][1000 genomes]
rs2884466	0.82[EUR][1000 genomes]
rs34080686	0.87[EUR][1000 genomes]
rs34212128	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34244392	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34447409	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34515259	0.84[EUR][1000 genomes]
rs34740542	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35556190	0.82[EUR][1000 genomes]
rs35872305	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs55814152	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57449872	0.82[AFR][1000 genomes]
rs6661987	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6667199	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73082432	0.82[AFR][1000 genomes]
rs7518399	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes]
rs7521041	0.86[ASN][1000 genomes]
rs7530292	0.93[YRI][hapmap]
rs7531219	0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs968531	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs968532	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999738	chr1:212218618-212513690	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv1009376	chr1:212292357-212680320	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
3	nsv549139	chr1:212332294-212876902	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv997629	chr1:212404489-212658785	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv535286	chr1:212404489-212658785	Strong transcription Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers 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	45 gene(s)	inside rSNPs	diseases
6	esv1799093	chr1:212447167-212468974	Enhancers Flanking Active TSS Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
7	esv1800932	chr1:212447167-212468974	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
8	esv1839997	chr1:212447167-212468974	Flanking Active TSS Weak transcription Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv873155	chr1:212449195-212502157	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
10	esv1839887	chr1:212457414-212478047	Enhancers Weak transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10863961	RP11-15I11.3	cis	lung	GTEx
rs10863961	RP11-15I11.3	cis	Thyroid	GTEx
rs10863961	RP11-15I11.3	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:81 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:212460200-212489200	Weak transcription	Spleen	Spleen
2	chr1:212461000-212469000	Enhancers	Brain Substantia Nigra	brain
3	chr1:212461000-212476200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr1:212461600-212468800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr1:212461800-212470200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:212462000-212471200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:212462200-212468800	Enhancers	Brain Anterior Caudate	brain
8	chr1:212462200-212471000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:212462200-212471000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
10	chr1:212462400-212469000	Enhancers	Brain Cingulate Gyrus	brain
11	chr1:212462600-212471000	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:212462800-212470000	Enhancers	Liver	Liver
13	chr1:212463600-212468800	Weak transcription	Thymus	Thymus
14	chr1:212463800-212471000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr1:212463800-212471000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr1:212464200-212471200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
17	chr1:212464200-212483000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
18	chr1:212464600-212473000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr1:212464800-212468600	Weak transcription	Gastric	stomach
20	chr1:212464800-212480200	Weak transcription	Lung	lung
21	chr1:212464800-212483800	Weak transcription	Pancreas	Pancrea
22	chr1:212464800-212506400	Weak transcription	Esophagus	oesophagus
23	chr1:212465000-212468200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr1:212465000-212468800	Weak transcription	Colonic Mucosa	Colon
25	chr1:212465000-212469600	Enhancers	Adipose Nuclei	Adipose
26	chr1:212465000-212470400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr1:212465000-212474800	Weak transcription	Osteobl	bone
28	chr1:212465000-212480200	Weak transcription	Primary hematopoietic stem cells	blood
29	chr1:212465200-212468200	Weak transcription	Right Ventricle	heart
30	chr1:212465200-212468400	Weak transcription	Hela-S3	cervix
31	chr1:212465400-212468200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr1:212465400-212475000	Weak transcription	Rectal Smooth Muscle	rectum
33	chr1:212465400-212482800	Weak transcription	Fetal Lung	lung
34	chr1:212465800-212483200	Weak transcription	Dnd41	blood
35	chr1:212466000-212468200	Weak transcription	Brain Angular Gyrus	brain
36	chr1:212466200-212468000	Weak transcription	Skeletal Muscle Female	skeletal muscle
37	chr1:212466200-212468200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr1:212466200-212468200	Weak transcription	Fetal Intestine Small	intestine
39	chr1:212466200-212468200	Weak transcription	Left Ventricle	heart
40	chr1:212466200-212468200	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr1:212466200-212468400	Enhancers	Primary T cells from cord blood	blood
42	chr1:212466200-212468400	Weak transcription	Right Atrium	heart
43	chr1:212466200-212468600	Weak transcription	Small Intestine	intestine
44	chr1:212466200-212470400	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr1:212466200-212470600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr1:212466200-212473000	Weak transcription	Primary T cells fromperipheralblood	blood
47	chr1:212466200-212506400	Weak transcription	Rectal Mucosa Donor 31	rectum
48	chr1:212466400-212468200	Weak transcription	Psoas Muscle	Psoas
49	chr1:212466400-212468600	Weak transcription	Aorta	Aorta
50	chr1:212466400-212470200	Weak transcription	Primary B cells from peripheral blood	blood

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