Variant report

Variant	rs9669404
Chromosome Location	chr12:46798963-46798964
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:46793862..46797366-chr12:46798440..46803120,6	MCF-7	breast:
2	chr12:46776484..46782223-chr12:46794471..46799373,6	MCF-7	breast:
3	chr12:46777252..46779393-chr12:46796903..46799597,3	MCF-7	breast:
4	chr12:46797323..46800132-chr12:46887352..46889333,2	MCF-7	breast:
5	chr12:46781039..46783581-chr12:46796813..46799166,3	K562	blood:
6	chr12:46778629..46780721-chr12:46796448..46799296,3	K562	blood:
7	chr12:46798219..46802284-chr12:46803095..46805948,4	K562	blood:

Variant related genes	Relation type
ENSG00000257496	Chromatin interaction
ENSG00000257261	Chromatin interaction

Extended variants
information (count: 128 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:123)

rs_ID	r²[population]
rs10748448	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10748450	0.87[EUR][1000 genomes]
rs10785627	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10785628	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs10785629	0.87[EUR][1000 genomes]
rs10880947	0.84[MEX][hapmap]
rs10880966	0.92[AMR][1000 genomes]
rs10880967	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10880968	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10880969	0.85[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10880970	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10880971	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10880973	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs10880974	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11183454	1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs11183467	0.81[ASW][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs11183478	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183479	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183482	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs11183483	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11183484	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11183488	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11183504	0.89[MEX][hapmap]
rs1125909	0.95[CEU][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11561535	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12099669	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12298616	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12299499	1.00[YRI][hapmap]
rs12313929	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs12314541	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12319162	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12321512	1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs12813763	0.89[MEX][hapmap];0.82[TSI][hapmap];0.86[AMR][1000 genomes]
rs12814298	0.80[AMR][1000 genomes]
rs12814341	0.86[AMR][1000 genomes]
rs12822345	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12824565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12832425	0.86[AMR][1000 genomes]
rs12832777	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13377959	0.81[ASW][hapmap];1.00[YRI][hapmap]
rs1472178	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1472179	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1492895	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17096884	0.81[YRI][hapmap]
rs17096922	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs2131371	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2220727	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2408497	0.94[AMR][1000 genomes]
rs2408498	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2897951	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3936214	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4072304	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4076247	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4077707	0.95[CEU][hapmap];0.85[CHB][hapmap];0.89[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap];0.93[TSI][hapmap];0.84[EUR][1000 genomes]
rs4077708	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4258438	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4427617	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768118	0.95[CEU][hapmap];0.90[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];0.81[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4768119	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768121	0.83[AMR][1000 genomes]
rs4768122	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4768123	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[EUR][1000 genomes]
rs4768699	0.82[CEU][hapmap];0.81[CHB][hapmap];0.92[CHD][hapmap];0.94[GIH][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs4768709	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4768710	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768711	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768712	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768713	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768714	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4768715	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768716	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4768717	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4768718	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768719	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4768723	1.00[CEU][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs4768724	0.87[EUR][1000 genomes]
rs4768725	0.87[EUR][1000 genomes]
rs4768727	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs4768730	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs6582641	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6582642	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6582643	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6582645	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6582646	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6582657	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs6582658	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes]
rs6582661	0.90[CHB][hapmap];0.94[JPT][hapmap]
rs6582663	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7134289	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7134505	0.83[ASN][1000 genomes]
rs7301001	0.83[AMR][1000 genomes]
rs7311504	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7312259	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7316127	0.84[MEX][hapmap]
rs73282591	0.83[AFR][1000 genomes]
rs7485580	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7485599	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7486495	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7486532	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7486580	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7486915	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs7487828	0.83[AMR][1000 genomes]
rs7487877	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7488144	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs7488450	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7489242	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7953450	0.85[ASN][1000 genomes]
rs7954314	0.81[ASW][hapmap];0.89[LWK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs7954645	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7956314	0.91[CHB][hapmap];0.90[JPT][hapmap]
rs7959731	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7960808	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs7964767	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs7967889	0.95[YRI][hapmap]
rs7968897	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7976280	0.82[TSI][hapmap];0.94[AMR][1000 genomes]
rs7980455	0.80[CEU][hapmap]
rs7980775	0.85[MEX][hapmap]
rs923788	1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs9706460	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs9706520	0.90[CHB][hapmap];0.95[JPT][hapmap]
rs9971879	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832398	chr12:46611692-46825530	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	181 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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:56 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:46779600-46802800	Weak transcription	Pancreas	Pancrea
2	chr12:46793800-46801200	Enhancers	Dnd41	blood
3	chr12:46794200-46799000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
4	chr12:46794200-46799000	Enhancers	Osteobl	bone
5	chr12:46794200-46799600	Enhancers	Primary T cells from cord blood	blood
6	chr12:46794400-46799000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
7	chr12:46794400-46799000	Enhancers	HSMMtube	muscle
8	chr12:46794400-46799000	Enhancers	NHLF	lung
9	chr12:46794800-46802200	Weak transcription	Placenta	Placenta
10	chr12:46795000-46809200	Weak transcription	Esophagus	oesophagus
11	chr12:46795800-46800200	Weak transcription	Adipose Nuclei	Adipose
12	chr12:46795800-46800200	Weak transcription	K562	blood
13	chr12:46795800-46804000	Weak transcription	Right Ventricle	heart
14	chr12:46796000-46799200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
15	chr12:46797000-46799400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
16	chr12:46797000-46819800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr12:46797200-46799400	Enhancers	NH-A	brain
18	chr12:46797400-46800600	Weak transcription	Stomach Smooth Muscle	stomach
19	chr12:46797600-46800600	Weak transcription	NHEK	skin
20	chr12:46797600-46800800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:46797600-46801200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
22	chr12:46797600-46802000	Weak transcription	Aorta	Aorta
23	chr12:46797800-46799000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr12:46797800-46800600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr12:46797800-46805400	Weak transcription	HepG2	liver
26	chr12:46798200-46800400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
27	chr12:46798400-46799200	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr12:46798400-46800800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr12:46798400-46802000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr12:46798400-46802400	Weak transcription	Fetal Lung	lung
31	chr12:46798600-46799600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr12:46798600-46799600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr12:46798600-46800200	Weak transcription	Psoas Muscle	Psoas
34	chr12:46798600-46800600	Weak transcription	HMEC	breast
35	chr12:46798600-46801600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
36	chr12:46798600-46801800	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr12:46798600-46802000	Weak transcription	Fetal Stomach	stomach
38	chr12:46798600-46802000	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:46798600-46802200	Weak transcription	Fetal Muscle Leg	muscle
40	chr12:46798600-46802200	Weak transcription	Left Ventricle	heart
41	chr12:46798600-46802600	Weak transcription	HUVEC	blood vessel
42	chr12:46798600-46807200	Weak transcription	Small Intestine	intestine
43	chr12:46798800-46799000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr12:46798800-46799000	Enhancers	Muscle Satellite Cultured Cells	--
45	chr12:46798800-46799000	Enhancers	GM12878-XiMat	blood
46	chr12:46798800-46799400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr12:46798800-46799800	Weak transcription	Rectal Smooth Muscle	rectum
48	chr12:46798800-46800200	Weak transcription	Fetal Heart	heart
49	chr12:46798800-46800400	Weak transcription	Right Atrium	heart
50	chr12:46798800-46800400	Weak transcription	NHDF-Ad	bronchial

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