Variant report

Variant	rs2764461
Chromosome Location	chr1:180256689-180256690
allele	C/G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180256674..180259200-chr1:180261718..180263635,2	MCF-7	breast:
2	chr1:180243286..180245062-chr1:180255906..180257505,2	MCF-7	breast:
3	chr1:180256515..180258678-chr1:180261672..180263403,2	K562	blood:
4	chr1:180252603..180254797-chr1:180256198..180258303,3	K562	blood:

Variant related genes	Relation type
ENSG00000230124	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:103)

rs_ID	r²[population]
rs10157891	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1072856	0.85[AFR][1000 genomes]
rs10733004	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes]
rs10733005	0.82[EUR][1000 genomes]
rs10737343	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737344	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10753210	1.00[ASN][1000 genomes]
rs10753213	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798744	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798749	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798763	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10798764	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913972	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10914011	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094597	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094598	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1094599	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12027553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12144149	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1361628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418100	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1418103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1591898	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1935283	1.00[ASN][1000 genomes]
rs1961741	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2153753	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2262371	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2764432	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764434	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764435	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764437	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764438	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764441	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764442	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764444	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764451	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764452	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764453	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2764454	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2764456	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764457	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764458	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764459	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764462	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764467	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2764468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794965	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2794966	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794967	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794968	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794969	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794970	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794971	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794972	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794973	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794974	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794975	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2794976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4259605	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4281291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4304539	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4333819	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4540612	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4609392	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4651061	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652501	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs4652502	0.92[EUR][1000 genomes]
rs61811560	1.00[ASN][1000 genomes]
rs6425620	1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425621	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425622	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425623	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425624	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425626	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6425630	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659147	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664944	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6669304	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677367	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6680754	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6682067	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6684842	1.00[ASN][1000 genomes]
rs6687873	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6691333	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6695360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs704334	1.00[JPT][hapmap]
rs7526743	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7530015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs7532972	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7543143	1.00[ASN][1000 genomes]
rs7546030	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822703	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822704	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs822705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs863720	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs863721	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880911	0.94[EUR][1000 genomes]
rs912766	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9425879	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1003739	chr1:180027760-180483292	Enhancers ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv535217	chr1:180027760-180483292	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
3	nsv832004	chr1:180128502-180335540	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv466239	chr1:180145978-180268476	Bivalent Enhancer ZNF genes & repeats Genic enhancers Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv548345	chr1:180145978-180268476	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
6	nsv1001477	chr1:180172903-180298287	Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv535220	chr1:180172903-180298287	Bivalent Enhancer ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv498075	chr1:180179441-180278544	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180231000-180257200	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:180236800-180257600	Weak transcription	Fetal Brain Male	brain
3	chr1:180239200-180257200	Weak transcription	Osteobl	bone
4	chr1:180240200-180259000	Weak transcription	Colon Smooth Muscle	Colon
5	chr1:180240800-180258200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:180240800-180259400	Weak transcription	HepG2	liver
7	chr1:180240800-180264000	Weak transcription	Small Intestine	intestine
8	chr1:180240800-180270800	Weak transcription	NHLF	lung
9	chr1:180241000-180259600	Weak transcription	NH-A	brain
10	chr1:180241200-180257000	Weak transcription	K562	blood
11	chr1:180242000-180268400	Weak transcription	NHDF-Ad	bronchial
12	chr1:180242600-180257200	Weak transcription	Brain Substantia Nigra	brain
13	chr1:180243600-180257200	Weak transcription	GM12878-XiMat	blood
14	chr1:180243800-180268200	Weak transcription	Pancreas	Pancrea
15	chr1:180244000-180257200	Weak transcription	Brain Hippocampus Middle	brain
16	chr1:180244000-180257400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr1:180244200-180257200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:180244200-180257800	Weak transcription	Brain Germinal Matrix	brain
19	chr1:180244200-180258200	Weak transcription	Rectal Mucosa Donor 31	rectum
20	chr1:180244200-180258400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr1:180244200-180263000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:180244200-180270400	Weak transcription	Muscle Satellite Cultured Cells	--
23	chr1:180244200-180278200	Weak transcription	HSMMtube	muscle
24	chr1:180244600-180257600	Weak transcription	Fetal Kidney	kidney
25	chr1:180244800-180257600	Weak transcription	Fetal Muscle Trunk	muscle
26	chr1:180245000-180259800	Weak transcription	Colonic Mucosa	Colon
27	chr1:180245200-180258200	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr1:180245200-180259200	Weak transcription	Spleen	Spleen
29	chr1:180245200-180261600	Weak transcription	Right Ventricle	heart
30	chr1:180245200-180282400	Weak transcription	Fetal Intestine Large	intestine
31	chr1:180245400-180257200	Weak transcription	Brain Cingulate Gyrus	brain
32	chr1:180245400-180268200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr1:180245400-180280400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr1:180245600-180257200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:180246000-180257600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr1:180246400-180258000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr1:180246600-180257400	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr1:180246800-180264200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr1:180247600-180262000	Weak transcription	Aorta	Aorta
40	chr1:180247800-180257400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
41	chr1:180247800-180257600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:180247800-180258800	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr1:180247800-180259200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
44	chr1:180247800-180259200	Weak transcription	Psoas Muscle	Psoas
45	chr1:180247800-180260000	Weak transcription	HUES48 Cell Line	embryonic stem cell
46	chr1:180247800-180263800	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr1:180247800-180284200	Weak transcription	Fetal Thymus	thymus
48	chr1:180248000-180256800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr1:180248000-180257000	Weak transcription	HSMM	muscle
50	chr1:180248000-180257400	Weak transcription	Brain Anterior Caudate	brain

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