Variant report

Variant	rs6580709
Chromosome Location	chr12:49768256-49768257
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:49758729..49761448-chr12:49766521..49769323,5	K562	blood:
2	chr12:49758626..49763128-chr12:49766731..49772616,9	K562	blood:
3	chr12:49759412..49761483-chr12:49767858..49769589,2	MCF-7	breast:
4	chr12:49728027..49730101-chr12:49766863..49769705,2	MCF-7	breast:
5	chr12:49763667..49766660-chr12:49767399..49772486,5	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123352	Chromatin interaction

Extended variants
information (count: 110 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10160947	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10161131	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10506284	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs10506285	1.00[JPT][hapmap]
rs10783314	0.93[CEU][hapmap];0.85[EUR][1000 genomes]
rs10875948	1.00[CHB][hapmap]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11168988	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169005	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.85[EUR][1000 genomes]
rs11169008	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs11169009	0.85[EUR][1000 genomes]
rs11169014	0.81[EUR][1000 genomes]
rs11169015	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169016	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169017	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169027	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169043	0.82[EUR][1000 genomes]
rs11169045	0.81[EUR][1000 genomes]
rs11169048	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs11169049	0.90[EUR][1000 genomes]
rs11169058	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169059	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.81[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs11169063	0.83[ASW][hapmap];0.94[GIH][hapmap];0.86[TSI][hapmap]
rs11611743	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11830144	1.00[CHD][hapmap]
rs11834161	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11835037	1.00[CHB][hapmap]
rs11837234	1.00[CHB][hapmap]
rs12296440	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.80[MKK][hapmap];0.96[TSI][hapmap];0.82[EUR][1000 genomes]
rs12299282	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12301632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12302036	0.83[ASN][1000 genomes]
rs12305716	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12306118	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306212	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306645	0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306866	1.00[JPT][hapmap]
rs12309053	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12310129	1.00[JPT][hapmap]
rs12315996	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12320284	1.00[CEU][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12322319	1.00[ASN][1000 genomes]
rs12322335	1.00[CHB][hapmap]
rs12322561	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12581343	1.00[CHB][hapmap]
rs12581428	1.00[CHB][hapmap]
rs17123696	1.00[JPT][hapmap]
rs17123751	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17123764	1.00[CHD][hapmap]
rs17123790	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17197593	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1874910	1.00[JPT][hapmap]
rs2236746	1.00[CHB][hapmap]
rs2270741	1.00[JPT][hapmap]
rs2272478	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28450055	1.00[ASN][1000 genomes]
rs3847764	1.00[CHB][hapmap]
rs4144469	1.00[JPT][hapmap]
rs57108124	1.00[ASN][1000 genomes]
rs57601151	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58095611	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs59250459	1.00[ASN][1000 genomes]
rs60808917	0.82[EUR][1000 genomes]
rs61340540	1.00[ASN][1000 genomes]
rs6580707	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580710	1.00[ASN][1000 genomes]
rs6580711	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6580715	0.81[EUR][1000 genomes]
rs6580716	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7132684	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133398	0.85[CEU][hapmap];0.90[GIH][hapmap];0.87[TSI][hapmap]
rs7139061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7294648	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7294973	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7295162	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7295247	1.00[CHB][hapmap]
rs7295556	0.93[CEU][hapmap];1.00[GIH][hapmap];0.97[TSI][hapmap];0.82[EUR][1000 genomes]
rs7309997	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs73295291	1.00[ASN][1000 genomes]
rs73295300	1.00[ASN][1000 genomes]
rs73297209	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73297210	1.00[ASN][1000 genomes]
rs73297243	1.00[ASN][1000 genomes]
rs7342318	1.00[CHB][hapmap]
rs7342365	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs7342384	1.00[CHB][hapmap]
rs74089066	1.00[ASN][1000 genomes]
rs7488923	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7955245	0.81[EUR][1000 genomes]
rs7955541	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961032	0.83[ASN][1000 genomes]
rs7962951	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969010	0.92[CEU][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970059	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7974420	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7975712	0.83[ASW][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap]
rs7976165	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs7980731	0.83[ASW][hapmap];0.93[CEU][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9919740	1.00[CHB][hapmap];1.00[JPT][hapmap]

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	nsv1051161	chr12:49314550-49828473	Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
2	nsv541489	chr12:49314550-49828473	Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	322 gene(s)	inside rSNPs	diseases
3	nsv1036452	chr12:49376285-49867760	Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	315 gene(s)	inside rSNPs	diseases
4	nsv1042122	chr12:49678529-49823168	Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Enhancers Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv1039176	chr12:49678529-49832618	Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
6	nsv899068	chr12:49714103-49924637	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv832405	chr12:49720279-49910862	Weak transcription Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
8	nsv899069	chr12:49760499-49924637	Strong transcription Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:60 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49761800-49790800	Weak transcription	Small Intestine	intestine
2	chr12:49762000-49771600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:49762200-49786200	Weak transcription	Primary T cells from cord blood	blood
4	chr12:49762800-49789600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr12:49763800-49768400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:49763800-49768400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr12:49763800-49770600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr12:49763800-49770600	Weak transcription	Fetal Intestine Large	intestine
9	chr12:49763800-49775600	Weak transcription	Ovary	ovary
10	chr12:49763800-49785600	Weak transcription	Thymus	Thymus
11	chr12:49763800-49791400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr12:49763800-49794200	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr12:49764000-49772400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr12:49764000-49775800	Weak transcription	Osteobl	bone
15	chr12:49764000-49781400	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr12:49764000-49782800	Weak transcription	Fetal Thymus	thymus
17	chr12:49764000-49797600	Weak transcription	Fetal Muscle Leg	muscle
18	chr12:49764000-49807400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr12:49764200-49768400	Weak transcription	NHLF	lung
20	chr12:49764200-49769200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr12:49764200-49769200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr12:49764200-49773800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr12:49764200-49781000	Weak transcription	K562	blood
24	chr12:49764200-49782600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:49764200-49786400	Weak transcription	HMEC	breast
26	chr12:49764200-49804200	Weak transcription	Primary B cells from cord blood	blood
27	chr12:49764200-49840200	Weak transcription	Fetal Lung	lung
28	chr12:49764400-49769200	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr12:49764400-49771000	Weak transcription	Fetal Kidney	kidney
30	chr12:49764400-49775400	Weak transcription	HUVEC	blood vessel
31	chr12:49764400-49775600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:49764400-49791400	Weak transcription	HSMM	muscle
33	chr12:49764400-49822200	Weak transcription	Muscle Satellite Cultured Cells	--
34	chr12:49764600-49783000	Weak transcription	Left Ventricle	heart
35	chr12:49764800-49768400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:49764800-49768400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr12:49764800-49790400	Weak transcription	Psoas Muscle	Psoas
38	chr12:49765200-49787400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr12:49765600-49768400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
40	chr12:49766000-49783200	Weak transcription	Hela-S3	cervix
41	chr12:49766400-49768400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr12:49766600-49822200	Weak transcription	NH-A	brain
43	chr12:49767000-49768400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr12:49767200-49783000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr12:49767400-49771000	Weak transcription	A549	lung
46	chr12:49767600-49769200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:49767600-49783000	Weak transcription	Fetal Brain Female	brain
48	chr12:49767600-49787800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr12:49767800-49768400	Strong transcription	Brain Germinal Matrix	brain
50	chr12:49767800-49782600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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