Variant report

Variant	rs12093073
Chromosome Location	chr1:180462683-180462684
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180455309..180463447-chr1:180464060..180473080,17	MCF-7	breast:
2	chr1:180459458..180461000-chr1:180461479..180464072,2	MCF-7	breast:
3	chr1:180461405..180464070-chr1:180746505..180748315,2	K562	blood:

Variant related genes	Relation type
ENSG00000135847	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10494528	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.91[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10494529	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10913988	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913990	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913991	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913995	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10913996	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10914004	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10914012	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11487431	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12058221	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12062561	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12065388	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12069389	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12070624	0.82[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12071353	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12076995	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12077656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12077791	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12077839	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12081494	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12083900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12084039	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12087060	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12087325	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12089373	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1339721	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs16856042	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4403592	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];0.80[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55660948	0.83[EUR][1000 genomes]
rs55962675	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56303477	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56333717	0.83[EUR][1000 genomes]
rs56747078	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57070632	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57424497	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57493263	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58145394	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs58369506	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59357483	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59371134	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60528279	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61024380	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425635	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6659477	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66619942	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6663823	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.92[TSI][hapmap];0.91[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6667388	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670242	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6670868	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs6670950	1.00[CEU][hapmap];0.83[MKK][hapmap]
rs6673113	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6676778	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs66913400	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6696075	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67071426	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67343454	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67517246	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67621570	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67623108	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67716213	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67830766	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs68010689	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68046305	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72714872	0.83[EUR][1000 genomes]
rs72714883	0.83[EUR][1000 genomes]
rs72714890	0.83[EUR][1000 genomes]
rs72714891	0.83[EUR][1000 genomes]
rs72714892	0.83[EUR][1000 genomes]
rs72714894	0.83[EUR][1000 genomes]
rs72714896	0.83[EUR][1000 genomes]
rs72716605	0.83[EUR][1000 genomes]
rs72716619	0.88[EUR][1000 genomes]
rs72716624	0.88[EUR][1000 genomes]
rs72716634	0.90[EUR][1000 genomes]
rs72716637	0.93[EUR][1000 genomes]
rs72720921	0.83[EUR][1000 genomes]
rs73037411	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73048237	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7533389	1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap]
rs7542223	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7552701	1.00[CEU][hapmap];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1013716	chr1:180287338-180477072	Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
4	nsv535221	chr1:180287338-180477072	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
5	esv2762200	chr1:180300936-180493841	ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
7	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180404400-180469000	Weak transcription	Pancreas	Pancrea
2	chr1:180428000-180470000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr1:180431200-180470200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr1:180432000-180470600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr1:180434000-180465600	Weak transcription	Fetal Brain Male	brain
6	chr1:180434200-180470200	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr1:180435200-180469000	Weak transcription	Brain Angular Gyrus	brain
8	chr1:180437600-180470400	Weak transcription	Right Ventricle	heart
9	chr1:180437600-180470600	Weak transcription	Spleen	Spleen
10	chr1:180437600-180471000	Weak transcription	Lung	lung
11	chr1:180440000-180469000	Weak transcription	HSMMtube	muscle
12	chr1:180440200-180468400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr1:180440200-180469000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr1:180441800-180462800	Weak transcription	NHLF	lung
15	chr1:180443400-180468200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:180444800-180470600	Weak transcription	Esophagus	oesophagus
17	chr1:180447000-180470400	Weak transcription	Colonic Mucosa	Colon
18	chr1:180447800-180469000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr1:180448400-180470200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr1:180449200-180469000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr1:180449400-180466800	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr1:180449800-180465600	Weak transcription	Fetal Brain Female	brain
23	chr1:180452000-180465200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
24	chr1:180452000-180469000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
25	chr1:180452000-180470000	Weak transcription	Fetal Heart	heart
26	chr1:180452200-180463400	Weak transcription	Brain Hippocampus Middle	brain
27	chr1:180452200-180467000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr1:180452400-180464000	Weak transcription	Colon Smooth Muscle	Colon
29	chr1:180453200-180467400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr1:180453800-180470600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:180454200-180463600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr1:180454400-180464800	Strong transcription	Primary T helper cells fromperipheralblood	blood
33	chr1:180454600-180470600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr1:180454800-180468600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr1:180455000-180468800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr1:180455200-180466600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr1:180455400-180470000	Weak transcription	Liver	Liver
38	chr1:180455600-180463000	Weak transcription	Fetal Thymus	thymus
39	chr1:180455600-180463000	Weak transcription	Ovary	ovary
40	chr1:180455600-180465400	Weak transcription	Duodenum Mucosa	Duodenum
41	chr1:180455600-180469000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr1:180455600-180469000	Weak transcription	Psoas Muscle	Psoas
43	chr1:180455600-180469000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr1:180455600-180469400	Weak transcription	Brain Inferior Temporal Lobe	brain
45	chr1:180455600-180469400	Weak transcription	Thymus	Thymus
46	chr1:180455600-180469600	Weak transcription	Gastric	stomach
47	chr1:180455600-180470200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr1:180455600-180470200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr1:180455600-180470200	Weak transcription	Brain Substantia Nigra	brain
50	chr1:180455600-180471000	Weak transcription	Left Ventricle	heart

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