Variant report

Variant	rs6580707
Chromosome Location	chr12:49763868-49763869
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:49656837..49661590-chr12:49759665..49765017,7	K562	blood:
2	chr12:49689044..49692243-chr12:49760659..49764012,4	MCF-7	breast:
3	chr12:49763667..49766660-chr12:49767399..49772486,5	MCF-7	breast:
4	chr12:49761628..49763980-chr12:49778457..49780387,2	K562	blood:
5	chr12:49760548..49762232-chr12:49762268..49764290,2	MCF-7	breast:
6	chr12:49763359..49766291-chr12:49781897..49784873,2	MCF-7	breast:
7	chr12:49757985..49760399-chr12:49762224..49765637,3	MCF-7	breast:
8	chr12:49762463..49764079-chr12:49764319..49766160,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000258101	Chromatin interaction
ENSG00000167553	Chromatin interaction
ENSG00000123352	Chromatin interaction
ENSG00000135406	Chromatin interaction
ENSG00000257954	Chromatin interaction

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:101)

rs_ID	r²[population]
rs10160947	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10161131	0.86[AMR][1000 genomes];0.96[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];0.84[EUR][1000 genomes]
rs10875948	1.00[CHB][hapmap]
rs10875958	0.80[EUR][1000 genomes]
rs11168967	1.00[CHB][hapmap]
rs11168981	1.00[JPT][hapmap];0.81[MEX][hapmap]
rs11168988	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[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];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs11169008	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs11169009	0.84[EUR][1000 genomes]
rs11169014	0.80[EUR][1000 genomes]
rs11169015	0.85[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];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.85[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	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169043	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];0.96[TSI][hapmap];0.92[EUR][1000 genomes]
rs11169049	0.89[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];0.93[TSI][hapmap]
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];0.96[TSI][hapmap]
rs11169063	0.83[ASW][hapmap];0.94[GIH][hapmap];0.83[TSI][hapmap]
rs11611743	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.93[TSI][hapmap]
rs12299282	0.83[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306212	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12306645	0.85[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12318618	1.00[CHB][hapmap]
rs12320284	1.00[CEU][hapmap];0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.93[YRI][hapmap];0.86[AMR][1000 genomes];0.96[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	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58095611	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs59250459	1.00[ASN][1000 genomes]
rs61340540	1.00[ASN][1000 genomes]
rs6580709	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	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[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	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7133398	0.85[CEU][hapmap];0.90[GIH][hapmap];0.90[TSI][hapmap]
rs7139061	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.92[YRI][hapmap];0.86[AMR][1000 genomes];0.96[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];0.93[TSI][hapmap];0.81[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];0.97[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];0.84[EUR][1000 genomes]
rs7955245	0.80[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[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];0.98[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7969010	0.92[CEU][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[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];0.95[LWK][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970059	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7974420	0.83[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7975712	0.83[ASW][hapmap];1.00[GIH][hapmap];0.90[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];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.81[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:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:49759800-49764000	Active TSS	Rectal Mucosa Donor 29	rectum
2	chr12:49761800-49764000	Flanking Active TSS	Hela-S3	cervix
3	chr12:49761800-49790800	Weak transcription	Small Intestine	intestine
4	chr12:49762000-49764200	Enhancers	Placenta Amnion	Placenta Amnion
5	chr12:49762000-49764600	Enhancers	Primary B cells from peripheral blood	blood
6	chr12:49762000-49766800	Weak transcription	Esophagus	oesophagus
7	chr12:49762000-49767200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr12:49762000-49771600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr12:49762200-49764200	Enhancers	Primary B cells from cord blood	blood
10	chr12:49762200-49786200	Weak transcription	Primary T cells from cord blood	blood
11	chr12:49762400-49764000	Enhancers	Fetal Intestine Small	intestine
12	chr12:49762400-49764000	Enhancers	Rectal Mucosa Donor 31	rectum
13	chr12:49762400-49764000	Flanking Active TSS	HUVEC	blood vessel
14	chr12:49762400-49764200	Enhancers	Fetal Lung	lung
15	chr12:49762600-49764000	Enhancers	iPS-15b Cell Line	embryonic stem cell
16	chr12:49762600-49764000	Enhancers	iPS-18 Cell Line	embryonic stem cell
17	chr12:49762600-49764000	Enhancers	Primary hematopoietic stem cells	blood
18	chr12:49762600-49764000	Enhancers	Adipose Nuclei	Adipose
19	chr12:49762600-49764000	Enhancers	Colon Smooth Muscle	Colon
20	chr12:49762600-49764000	Enhancers	Fetal Brain Male	brain
21	chr12:49762600-49764200	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr12:49762600-49764200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr12:49762600-49764200	Enhancers	Fetal Heart	heart
24	chr12:49762600-49764400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
25	chr12:49762600-49765000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr12:49762800-49764000	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr12:49762800-49764000	Enhancers	Brain Anterior Caudate	brain
28	chr12:49762800-49764000	Enhancers	Dnd41	blood
29	chr12:49762800-49764200	Flanking Active TSS	NHEK	skin
30	chr12:49762800-49764800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr12:49762800-49764800	Enhancers	Psoas Muscle	Psoas
32	chr12:49762800-49766400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
33	chr12:49762800-49789600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr12:49763000-49764000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr12:49763000-49764000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:49763000-49764000	Enhancers	Fetal Muscle Trunk	muscle
37	chr12:49763000-49764000	Enhancers	Fetal Muscle Leg	muscle
38	chr12:49763000-49764000	Enhancers	Fetal Thymus	thymus
39	chr12:49763000-49764000	Enhancers	Left Ventricle	heart
40	chr12:49763000-49764200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
41	chr12:49763000-49764200	Flanking Active TSS	A549	lung
42	chr12:49763200-49764000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:49763200-49764000	Enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr12:49763200-49764000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr12:49763200-49764000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
46	chr12:49763200-49764000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr12:49763200-49764000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
48	chr12:49763200-49764000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
49	chr12:49763200-49764200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr12:49763200-49764400	Enhancers	HSMM	muscle

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