Variant report

Variant	rs10880974
Chromosome Location	chr12:46871058-46871059
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46758281..46761226-chr12:46870849..46874065,3	K562	blood:
2	chr12:46775882..46782891-chr12:46867252..46874732,11	MCF-7	breast:
3	chr12:46750575..46752943-chr12:46867557..46871198,3	K562	blood:
4	chr12:46870046..46873030-chr12:46878483..46880314,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000134294	Chromatin interaction
ENSG00000257496	Chromatin interaction
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10748448	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs10748450	0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs10785628	0.85[AMR][1000 genomes]
rs10785629	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs10880973	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11183486	0.94[CHB][hapmap];0.89[JPT][hapmap]
rs11183500	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11183502	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11183503	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11183504	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11837427	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12313929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12314541	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs12824565	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12827740	0.83[AMR][1000 genomes]
rs2252238	0.95[CEU][hapmap]
rs3925101	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4077707	0.85[CHB][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4077708	0.85[AMR][1000 genomes]
rs4768118	0.80[CHB][hapmap]
rs4768123	0.85[AMR][1000 genomes]
rs4768699	0.90[JPT][hapmap]
rs4768723	0.85[AMR][1000 genomes]
rs4768724	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768725	0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs4768726	0.95[CEU][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768727	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768728	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768729	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4768730	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768733	0.95[CEU][hapmap]
rs6582645	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs6582657	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6582658	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6582659	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6582660	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582661	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582663	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7486915	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488144	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7488577	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7954645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7956314	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7959731	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7960808	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964767	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7980455	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9669404	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9706162	1.00[CEU][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9706460	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9706520	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9971879	0.91[CHB][hapmap];0.95[JPT][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:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr12:46864200-46877400	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr12:46864400-46877400	Weak transcription	Primary T cells from cord blood	blood
4	chr12:46865400-46879200	Weak transcription	Right Ventricle	heart
5	chr12:46866400-46871400	Weak transcription	Dnd41	blood
6	chr12:46867800-46871600	Weak transcription	Fetal Thymus	thymus
7	chr12:46867800-46873400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr12:46867800-46875800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
9	chr12:46868000-46872200	Enhancers	HepG2	liver
10	chr12:46868000-46876200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:46868000-46876200	Weak transcription	Primary B cells from cord blood	blood
12	chr12:46868000-46876400	Weak transcription	K562	blood
13	chr12:46868000-46881200	Weak transcription	GM12878-XiMat	blood
14	chr12:46868000-46883200	Weak transcription	Fetal Heart	heart
15	chr12:46868200-46877400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr12:46868200-46879200	Weak transcription	Primary B cells from peripheral blood	blood
17	chr12:46868400-46871200	Weak transcription	Rectal Mucosa Donor 31	rectum
18	chr12:46868600-46871200	Weak transcription	Osteobl	bone
19	chr12:46868600-46872400	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:46868600-46872600	Weak transcription	Primary monocytes fromperipheralblood	blood
21	chr12:46868600-46872800	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr12:46868600-46874000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:46868600-46874000	Weak transcription	Pancreas	Pancrea
24	chr12:46868600-46874000	Weak transcription	NHDF-Ad	bronchial
25	chr12:46868600-46874000	Weak transcription	NHEK	skin
26	chr12:46868600-46874200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:46868600-46877400	Weak transcription	Fetal Intestine Small	intestine
28	chr12:46868600-46877400	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr12:46868600-46877600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:46868600-46877600	Weak transcription	Ovary	ovary
31	chr12:46868600-46883000	Weak transcription	Left Ventricle	heart
32	chr12:46868600-46883400	Weak transcription	Psoas Muscle	Psoas
33	chr12:46868600-46889200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr12:46868800-46871400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr12:46868800-46876600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr12:46868800-46883400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:46868800-46886000	Weak transcription	HSMMtube	muscle
38	chr12:46869000-46871400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:46869200-46872800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr12:46869200-46876400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr12:46869200-46876800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr12:46869800-46872200	Enhancers	Hela-S3	cervix
43	chr12:46870000-46872000	Enhancers	A549	lung
44	chr12:46870400-46872000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr12:46870400-46880400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
46	chr12:46870600-46872000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
47	chr12:46871000-46871200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
48	chr12:46871000-46871200	Enhancers	Esophagus	oesophagus
49	chr12:46871000-46871200	Enhancers	Gastric	stomach
50	chr12:46871000-46872000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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