Variant report

Variant	rs7980455
Chromosome Location	chr12:46860506-46860507
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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	chr12:46764216..46766970-chr12:46858797..46861757,2	K562	blood:
7	chr12:46859836..46862512-chr12:46864660..46866357,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000258096	Chromatin interaction
ENSG00000134294	Chromatin interaction

Extended variants
information (count: 68 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10748450	0.88[AMR][1000 genomes]
rs10785628	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10785629	0.88[AMR][1000 genomes]
rs10880969	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs10880973	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs10880974	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11183456	1.00[CHB][hapmap]
rs11183478	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183479	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11183483	0.80[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs11183486	0.82[CEU][hapmap]
rs11183502	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[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];0.97[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];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1125909	1.00[CHB][hapmap];0.90[JPT][hapmap]
rs11837427	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12313929	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12314541	0.82[CEU][hapmap]
rs12824565	0.80[CEU][hapmap]
rs12827740	0.82[AMR][1000 genomes]
rs1472178	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2045556	0.89[CHB][hapmap]
rs2131371	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2252238	0.95[CEU][hapmap]
rs2897951	0.81[CEU][hapmap]
rs3925101	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs3936214	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4077707	0.80[CEU][hapmap];0.92[AMR][1000 genomes]
rs4077708	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4258438	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4427617	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768123	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4768709	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768716	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4768723	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4768724	0.88[AMR][1000 genomes]
rs4768725	0.88[AMR][1000 genomes]
rs4768726	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768727	1.00[CEU][hapmap];0.94[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];1.00[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];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768730	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582645	0.81[CEU][hapmap]
rs6582657	0.80[CEU][hapmap];0.88[AMR][1000 genomes]
rs6582658	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs6582659	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]
rs6582660	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6582661	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582663	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7485599	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7486915	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7488144	1.00[CEU][hapmap];0.94[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7954645	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7956314	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7959731	0.80[CEU][hapmap]
rs7960808	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7964767	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9669404	0.80[CEU][hapmap]
rs9706162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9706460	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706520	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9971879	0.80[CEU][hapmap]

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:39 , 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	chr12:46854200-46860800	Weak transcription	HUVEC	blood vessel
6	chr12:46854800-46864000	Weak transcription	Spleen	Spleen
7	chr12:46854800-46866000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr12:46855000-46863800	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:46855400-46863600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:46855400-46863800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr12:46855600-46863400	Weak transcription	Primary B cells from peripheral blood	blood
12	chr12:46855800-46864000	Weak transcription	Colon Smooth Muscle	Colon
13	chr12:46856000-46864000	Weak transcription	Right Ventricle	heart
14	chr12:46856000-46864800	Weak transcription	Small Intestine	intestine
15	chr12:46856000-46867800	Weak transcription	Aorta	Aorta
16	chr12:46856200-46862000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr12:46856200-46866000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
18	chr12:46856200-46866200	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr12:46856200-46868200	Weak transcription	Sigmoid Colon	Sigmoid Colon
20	chr12:46856600-46867400	Weak transcription	Placenta	Placenta
21	chr12:46857000-46864000	Weak transcription	NHDF-Ad	bronchial
22	chr12:46857200-46861400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr12:46857200-46861400	Weak transcription	Fetal Heart	heart
24	chr12:46857800-46864800	Weak transcription	Ovary	ovary
25	chr12:46858800-46867400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
26	chr12:46859000-46861200	Enhancers	HepG2	liver
27	chr12:46859000-46863200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr12:46859600-46861000	Weak transcription	Primary monocytes fromperipheralblood	blood
29	chr12:46859600-46862200	Weak transcription	Stomach Mucosa	stomach
30	chr12:46860000-46861000	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr12:46860000-46864000	Weak transcription	Right Atrium	heart
32	chr12:46860000-46866000	Weak transcription	K562	blood
33	chr12:46860000-46866200	Weak transcription	Fetal Intestine Small	intestine
34	chr12:46860200-46861600	Enhancers	GM12878-XiMat	blood
35	chr12:46860200-46867400	Enhancers	Hela-S3	cervix
36	chr12:46860400-46860800	Weak transcription	Primary B cells from cord blood	blood
37	chr12:46860400-46860800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:46860400-46861000	Weak transcription	Left Ventricle	heart
39	chr12:46860400-46864000	Weak transcription	Psoas Muscle	Psoas

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