Variant report

Variant	rs12042562
Chromosome Location	chr1:153856364-153856365
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:153849989..153852595-chr1:153855746..153857294,2	MCF-7	breast:
2	chr1:153854622..153856492-chr1:153859608..153861522,2	K562	blood:
3	chr1:153854488..153856914-chr1:153893554..153896712,3	K562	blood:

Variant related genes	Relation type
ENSG00000143614	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:100)

rs_ID	r²[population]
rs10127983	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1043608	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10559	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10796968	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10908557	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10908558	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10908627	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs1110165	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264532	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264559	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264567	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264619	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264620	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11264680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11264734	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11264743	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11264763	0.92[ASN][1000 genomes]
rs11264866	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264871	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264873	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264875	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264886	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264964	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11264974	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11265040	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11577942	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11581644	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11583152	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11585416	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11586075	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586593	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11586701	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs11586830	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587151	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11589043	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11589857	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11590099	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11591134	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022158	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12022730	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12023699	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12027783	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12028398	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12032914	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12033835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12038577	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12041850	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12041920	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12042989	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12043350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12048137	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12401565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403956	0.94[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12406003	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12409811	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12564669	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs12567313	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1572788	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34805562	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3748848	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3748849	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3791187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4391701	0.81[EUR][1000 genomes]
rs4508047	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4520447	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4595397	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4612664	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845357	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845358	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845576	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4845578	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4845583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4845585	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58095661	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59308681	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59678326	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs60150125	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61219911	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6427329	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6659220	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6666703	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6671132	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672856	0.87[CHB][hapmap];1.00[JPT][hapmap]
rs6680140	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6694061	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6700451	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6701341	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs6724	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72694231	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72694234	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7512766	0.83[EUR][1000 genomes]
rs7521303	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs7524739	0.86[ASN][1000 genomes]
rs7537691	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7547663	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7552274	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7552737	0.88[CHB][hapmap];0.93[JPT][hapmap]
rs8450	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs946682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9660089	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999364	chr1:153622634-154419436	Strong transcription Genic enhancers Flanking Active TSS Active TSS Weak transcription Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
2	nsv535175	chr1:153622634-154419436	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	286 gene(s)	inside rSNPs	diseases
3	nsv531892	chr1:153671910-153954090	Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv817392	chr1:153724807-153870005	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv532551	chr1:153732039-154192279	Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	233 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:153825800-153887200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:153830200-153863600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr1:153837000-153893000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr1:153842400-153859400	Weak transcription	Hela-S3	cervix
5	chr1:153842600-153862400	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr1:153842800-153862800	Weak transcription	Thymus	Thymus
7	chr1:153846200-153894200	Weak transcription	Esophagus	oesophagus
8	chr1:153846400-153871600	Weak transcription	Lung	lung
9	chr1:153849800-153859200	Weak transcription	Psoas Muscle	Psoas
10	chr1:153850200-153858600	Weak transcription	Dnd41	blood
11	chr1:153850800-153856400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
12	chr1:153852200-153856400	Enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr1:153852400-153856400	Enhancers	Primary T helper cells PMA-I stimulated	--
14	chr1:153853000-153856400	Enhancers	Primary T helper cells fromperipheralblood	blood
15	chr1:153853400-153856600	Enhancers	K562	blood
16	chr1:153853800-153864800	Weak transcription	Primary B cells from cord blood	blood
17	chr1:153853800-153892200	Weak transcription	Pancreas	Pancrea
18	chr1:153853800-153893400	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr1:153854000-153859800	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr1:153854000-153869200	Weak transcription	HepG2	liver
21	chr1:153854000-153892600	Weak transcription	Colonic Mucosa	Colon
22	chr1:153854200-153856600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
23	chr1:153854200-153858800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr1:153854200-153859400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr1:153854400-153856600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr1:153854400-153876200	Weak transcription	Spleen	Spleen
27	chr1:153854400-153892400	Weak transcription	Aorta	Aorta
28	chr1:153854600-153856400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr1:153854600-153856400	Enhancers	Fetal Intestine Small	intestine
30	chr1:153854600-153856800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr1:153854600-153859400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr1:153854600-153859800	Weak transcription	Placenta	Placenta
33	chr1:153854600-153865200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:153854600-153892200	Weak transcription	HSMM	muscle
35	chr1:153854800-153856400	Enhancers	Brain Hippocampus Middle	brain
36	chr1:153854800-153871200	Weak transcription	Fetal Muscle Trunk	muscle
37	chr1:153855000-153856400	Enhancers	Primary T cells from cord blood	blood
38	chr1:153855000-153857600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr1:153855000-153858400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr1:153855000-153859000	Weak transcription	Fetal Thymus	thymus
41	chr1:153855000-153859400	Weak transcription	Muscle Satellite Cultured Cells	--
42	chr1:153855000-153861600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr1:153855000-153866200	Weak transcription	Left Ventricle	heart
44	chr1:153855000-153886800	Weak transcription	Gastric	stomach
45	chr1:153855000-153886800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr1:153855000-153887200	Weak transcription	Ovary	ovary
47	chr1:153855000-153891800	Weak transcription	NHEK	skin
48	chr1:153855000-153892400	Weak transcription	NHLF	lung
49	chr1:153855000-153892800	Weak transcription	NH-A	brain
50	chr1:153855200-153856400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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