Variant report

Variant	rs6582659
Chromosome Location	chr12:46861409-46861410
allele	G/T
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:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46851276..46855951-chr12:46856514..46861457,9	K562	blood:
2	chr12:46859540..46862018-chr12:46919142..46921108,2	K562	blood:
3	chr12:46854831..46858483-chr12:46859173..46862265,4	MCF-7	breast:
4	chr12:46763112..46768883-chr12:46857331..46862698,8	K562	blood:
5	chr12:46852229..46855814-chr12:46857217..46861777,7	K562	blood:
6	chr12:46765375..46766918-chr12:46861342..46864304,2	MCF-7	breast:
7	chr12:46749620..46752358-chr12:46860774..46862635,2	MCF-7	breast:
8	chr12:46764216..46766970-chr12:46858797..46861757,2	K562	blood:
9	chr12:46859836..46862512-chr12:46864660..46866357,2	MCF-7	breast:
10	chr12:46857414..46859341-chr12:46861249..46864836,4	K562	blood:

No data

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10748450	0.83[AMR][1000 genomes]
rs10785628	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10785629	0.83[AMR][1000 genomes]
rs10880969	0.88[CHB][hapmap];0.88[JPT][hapmap]
rs10880973	0.83[AMR][1000 genomes]
rs10880974	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183479	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183483	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183502	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11183503	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11183504	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125909	1.00[CHB][hapmap];0.91[JPT][hapmap]
rs11837427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313929	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1472178	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2045556	0.89[CHB][hapmap]
rs2131371	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2252238	0.95[CEU][hapmap]
rs3925101	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3936214	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4077707	0.87[AMR][1000 genomes]
rs4077708	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4258438	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4427617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768123	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768709	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768716	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768723	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4768724	0.83[AMR][1000 genomes]
rs4768725	0.83[AMR][1000 genomes]
rs4768726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768727	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768728	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768730	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582657	0.83[AMR][1000 genomes]
rs6582658	0.83[AMR][1000 genomes]
rs6582660	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582661	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582663	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7486915	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7488144	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7488577	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954645	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7956314	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7960808	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964767	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7980455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9706162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9706460	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706520	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1842882	chr12:46691487-47009428	Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Genic enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	149 gene(s)	inside rSNPs	diseases
2	nsv1049525	chr12:46721742-47264172	Enhancers Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
3	nsv541486	chr12:46721742-47264172	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	152 gene(s)	inside rSNPs	diseases
4	esv3429861	chr12:46762813-46988789	Flanking Active TSS Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	145 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
2	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr12:46853200-46867400	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr12:46853800-46862600	Enhancers	Skeletal Muscle Male	skeletal muscle
5	chr12:46854800-46864000	Weak transcription	Spleen	Spleen
6	chr12:46854800-46866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr12:46855000-46863800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr12:46855400-46863600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
9	chr12:46855400-46863800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr12:46855600-46863400	Weak transcription	Primary B cells from peripheral blood	blood
11	chr12:46855800-46864000	Weak transcription	Colon Smooth Muscle	Colon
12	chr12:46856000-46864000	Weak transcription	Right Ventricle	heart
13	chr12:46856000-46864800	Weak transcription	Small Intestine	intestine
14	chr12:46856000-46867800	Weak transcription	Aorta	Aorta
15	chr12:46856200-46862000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr12:46856200-46866000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr12:46856200-46866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr12:46856600-46867400	Weak transcription	Placenta	Placenta
20	chr12:46857000-46864000	Weak transcription	NHDF-Ad	bronchial
21	chr12:46857800-46864800	Weak transcription	Ovary	ovary
22	chr12:46858800-46867400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr12:46859000-46863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr12:46859600-46862200	Weak transcription	Stomach Mucosa	stomach
25	chr12:46860000-46864000	Weak transcription	Right Atrium	heart
26	chr12:46860000-46866000	Weak transcription	K562	blood
27	chr12:46860000-46866200	Weak transcription	Fetal Intestine Small	intestine
28	chr12:46860200-46861600	Enhancers	GM12878-XiMat	blood
29	chr12:46860200-46867400	Enhancers	Hela-S3	cervix
30	chr12:46860400-46864000	Weak transcription	Psoas Muscle	Psoas
31	chr12:46860800-46861600	Enhancers	Primary B cells from cord blood	blood
32	chr12:46860800-46861600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr12:46860800-46866800	Enhancers	HUVEC	blood vessel
34	chr12:46861000-46861600	Enhancers	Primary monocytes fromperipheralblood	blood
35	chr12:46861000-46861600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr12:46861000-46861800	Enhancers	Left Ventricle	heart
37	chr12:46861000-46862200	Enhancers	Skeletal Muscle Female	skeletal muscle
38	chr12:46861000-46862600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
39	chr12:46861200-46862000	Weak transcription	HepG2	liver
40	chr12:46861200-46863400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:46861200-46863800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr12:46861200-46867000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr12:46861400-46861600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr12:46861400-46861600	Enhancers	NHEK	skin
45	chr12:46861400-46862200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr12:46861400-46862400	Enhancers	Fetal Heart	heart
47	chr12:46861400-46863600	Weak transcription	Primary T cells from cord blood	blood
48	chr12:46861400-46866600	Enhancers	A549	lung

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