Variant report

Variant	rs10880973
Chromosome Location	chr12:46853209-46853210
allele	A/C
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:46852729..46855589-chr12:46856810..46858940,4	MCF-7	breast:
2	chr12:46850217..46852233-chr12:46852801..46856137,3	K562	blood:
3	chr12:46853187..46855713-chr12:46867709..46870623,2	K562	blood:
4	chr12:46751305..46752826-chr12:46853204..46855628,2	K562	blood:
5	chr12:46749869..46752805-chr12:46853204..46855890,2	K562	blood:
6	chr12:46851276..46855951-chr12:46856514..46861457,9	K562	blood:
7	chr12:46852229..46855814-chr12:46857217..46861777,7	K562	blood:
8	chr12:46841282..46844144-chr12:46852953..46855040,2	K562	blood:
9	chr12:46765219..46768267-chr12:46847099..46854235,10	MCF-7	breast:
10	chr12:46662340..46664615-chr12:46852453..46854760,2	MCF-7	breast:
11	chr12:46846174..46847804-chr12:46851109..46853712,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000111371	Chromatin interaction
ENSG00000134294	Chromatin interaction
ENSG00000258096	Chromatin interaction

Extended variants
information (count: 111 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:107)

rs_ID	r²[population]
rs10748448	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.87[EUR][1000 genomes]
rs10748450	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10785627	0.88[EUR][1000 genomes]
rs10785628	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10785629	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10880967	0.87[EUR][1000 genomes]
rs10880968	0.87[EUR][1000 genomes]
rs10880969	0.86[CEU][hapmap];0.87[EUR][1000 genomes]
rs10880970	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10880971	0.91[EUR][1000 genomes]
rs10880974	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11183478	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183479	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183483	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs11183484	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11183488	0.91[EUR][1000 genomes]
rs11183502	0.88[AMR][1000 genomes]
rs11183503	0.86[AMR][1000 genomes]
rs11183504	0.86[AMR][1000 genomes]
rs1125909	0.95[CEU][hapmap];0.82[EUR][1000 genomes]
rs11837427	0.88[AMR][1000 genomes]
rs12099669	0.84[EUR][1000 genomes]
rs12298616	0.90[EUR][1000 genomes]
rs12313929	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12314541	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs12319162	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12321960	0.81[YRI][hapmap]
rs12822345	0.86[EUR][1000 genomes]
rs12824565	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.86[EUR][1000 genomes]
rs12827740	0.93[AMR][1000 genomes]
rs12832777	0.87[EUR][1000 genomes]
rs1472178	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs1472179	0.85[EUR][1000 genomes]
rs1492895	0.87[EUR][1000 genomes]
rs2131371	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2220727	0.87[EUR][1000 genomes]
rs2408498	0.87[EUR][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[EUR][1000 genomes]
rs3925101	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3936214	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs4072304	0.87[EUR][1000 genomes]
rs4076247	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4077708	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4427617	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes]
rs4768119	0.86[EUR][1000 genomes]
rs4768122	0.87[EUR][1000 genomes]
rs4768123	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.95[JPT][hapmap]
rs4768709	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768710	0.87[EUR][1000 genomes]
rs4768711	0.81[EUR][1000 genomes]
rs4768712	0.87[EUR][1000 genomes]
rs4768713	0.88[EUR][1000 genomes]
rs4768714	0.88[EUR][1000 genomes]
rs4768716	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4768717	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768718	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4768719	0.91[EUR][1000 genomes]
rs4768723	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768724	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768725	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4768726	0.88[AMR][1000 genomes]
rs4768727	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4768728	0.88[AMR][1000 genomes]
rs4768729	0.88[AMR][1000 genomes]
rs4768730	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6582641	0.82[EUR][1000 genomes]
rs6582643	0.81[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[EUR][1000 genomes]
rs6582646	0.87[EUR][1000 genomes]
rs6582657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6582658	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6582659	0.83[AMR][1000 genomes]
rs6582660	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6582661	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs6582663	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7134289	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7311504	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7312259	0.85[EUR][1000 genomes]
rs7485580	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7485599	0.86[EUR][1000 genomes]
rs7486495	0.88[EUR][1000 genomes]
rs7486532	0.91[EUR][1000 genomes]
rs7486580	0.88[EUR][1000 genomes]
rs7486915	0.91[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7487877	0.86[EUR][1000 genomes]
rs7488144	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7488450	0.87[EUR][1000 genomes]
rs7488577	0.88[AMR][1000 genomes]
rs7489242	0.87[EUR][1000 genomes]
rs7954645	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7956314	0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7959731	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7960808	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7964767	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs7968897	0.87[EUR][1000 genomes]
rs7980455	0.82[CEU][hapmap];0.88[AMR][1000 genomes]
rs9669403	0.84[YRI][hapmap]
rs9669404	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs9706162	0.88[AMR][1000 genomes]
rs9706460	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9706520	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs9971879	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[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:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46828000-46856000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:46844600-46854000	Weak transcription	Fetal Intestine Small	intestine
3	chr12:46844600-46854600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr12:46844600-46854800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr12:46844600-46855200	Weak transcription	Right Ventricle	heart
6	chr12:46844600-46866000	Weak transcription	Fetal Intestine Large	intestine
7	chr12:46844600-46886000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr12:46844800-46855200	Weak transcription	Colon Smooth Muscle	Colon
9	chr12:46845400-46855600	Enhancers	HepG2	liver
10	chr12:46847800-46853800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr12:46848400-46853800	Enhancers	Primary T cells from cord blood	blood
12	chr12:46849800-46854000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr12:46850000-46853800	Weak transcription	Fetal Heart	heart
14	chr12:46850000-46854000	Weak transcription	Gastric	stomach
15	chr12:46850000-46854600	Weak transcription	Psoas Muscle	Psoas
16	chr12:46850000-46860200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr12:46850200-46853400	Weak transcription	Right Atrium	heart
18	chr12:46850200-46853800	Weak transcription	Placenta	Placenta
19	chr12:46850200-46854400	Weak transcription	Small Intestine	intestine
20	chr12:46850200-46854800	Weak transcription	Fetal Kidney	kidney
21	chr12:46850200-46855200	Weak transcription	HSMMtube	muscle
22	chr12:46850400-46855200	Weak transcription	HSMM	muscle
23	chr12:46850400-46855800	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:46850400-46855800	Weak transcription	HMEC	breast
25	chr12:46850600-46853600	Weak transcription	Fetal Stomach	stomach
26	chr12:46850600-46853800	Weak transcription	Fetal Lung	lung
27	chr12:46850600-46853800	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr12:46850600-46854600	Weak transcription	Placenta Amnion	Placenta Amnion
29	chr12:46850600-46855000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr12:46850600-46859200	Weak transcription	Stomach Mucosa	stomach
31	chr12:46850800-46854600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr12:46851000-46854800	Weak transcription	A549	lung
33	chr12:46851400-46854000	Enhancers	Primary T helper cells fromperipheralblood	blood
34	chr12:46851600-46853400	Enhancers	Primary neutrophils fromperipheralblood	blood
35	chr12:46851600-46855400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr12:46851600-46855400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
37	chr12:46851800-46853400	Enhancers	Sigmoid Colon	Sigmoid Colon
38	chr12:46851800-46853800	Enhancers	Primary B cells from peripheral blood	blood
39	chr12:46851800-46853800	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr12:46851800-46853800	Enhancers	Primary T killer memory cells from peripheral blood	blood
41	chr12:46851800-46854000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
42	chr12:46851800-46854200	Enhancers	H1 Cell Line	embryonic stem cell
43	chr12:46851800-46854800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr12:46851800-46854800	Enhancers	Primary monocytes fromperipheralblood	blood
45	chr12:46851800-46855400	Enhancers	Primary hematopoietic stem cells	blood
46	chr12:46852000-46853800	Enhancers	Primary hematopoietic stem cells short term culture	blood
47	chr12:46852000-46853800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr12:46852000-46854000	Enhancers	ES-I3 Cell Line	embryonic stem cell
49	chr12:46852000-46854000	Enhancers	HUES64 Cell Line	embryonic stem cell
50	chr12:46852000-46854200	Enhancers	HUES6 Cell Line	embryonic stem cell

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