Variant report

Variant	rs12331562
Chromosome Location	chr4:148789141-148789142
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:148605054..148606838-chr4:148786766..148789557,2	MCF-7	breast:
2	chr4:148517547..148518065-chr4:148788601..148789204,2	MCF-7	breast:
3	chr4:148509882..148511690-chr4:148787031..148789794,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000164169	Chromatin interaction

Extended variants
information (count: 86 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10000278	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10001688	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10001756	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10003507	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10004138	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs10004691	0.92[EUR][1000 genomes]
rs10004792	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10014593	0.88[EUR][1000 genomes]
rs10014696	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10015875	0.94[EUR][1000 genomes]
rs10018820	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs10018903	0.82[CEU][hapmap]
rs10025069	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs10026985	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10030358	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs10049932	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs11099671	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs11099672	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11734553	0.82[EUR][1000 genomes]
rs11735412	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12509618	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs12513192	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs12641291	0.82[CEU][hapmap]
rs12643550	0.85[EUR][1000 genomes]
rs12650219	0.82[CEU][hapmap]
rs13129325	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13151898	0.92[EUR][1000 genomes]
rs1369958	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs17024037	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17613979	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17614025	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs17676080	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2043643	0.92[EUR][1000 genomes]
rs2043644	0.82[CEU][hapmap]
rs2043645	0.92[EUR][1000 genomes]
rs28576385	0.94[EUR][1000 genomes]
rs28614116	0.92[EUR][1000 genomes]
rs2884400	0.90[EUR][1000 genomes]
rs34970355	0.82[EUR][1000 genomes]
rs35243600	0.92[EUR][1000 genomes]
rs35810358	0.98[EUR][1000 genomes]
rs35899247	0.92[EUR][1000 genomes]
rs3893175	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3990920	1.00[CEU][hapmap];0.87[EUR][1000 genomes]
rs4240338	0.82[CEU][hapmap]
rs4240339	0.82[CEU][hapmap]
rs4240341	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs4491995	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs4571312	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs4627844	0.82[EUR][1000 genomes]
rs4835103	0.82[CEU][hapmap];0.89[EUR][1000 genomes]
rs4835109	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs4835110	0.85[EUR][1000 genomes]
rs4835469	0.82[CEU][hapmap]
rs55820558	0.92[EUR][1000 genomes]
rs62330732	0.87[EUR][1000 genomes]
rs62330735	0.87[EUR][1000 genomes]
rs62330737	0.84[EUR][1000 genomes]
rs6535569	0.82[EUR][1000 genomes]
rs6811769	0.82[EUR][1000 genomes]
rs6818371	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6832527	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6840771	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs6843392	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs6856273	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7656471	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7660508	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs7666127	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs7677632	0.92[EUR][1000 genomes]
rs7698670	0.94[EUR][1000 genomes]
rs893022	0.82[CEU][hapmap]
rs893033	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs9991741	1.00[CEU][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9994650	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs9995896	0.82[CEU][hapmap]
rs9995956	1.00[CEU][hapmap];0.95[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9996108	0.82[CEU][hapmap]
rs9996209	0.82[EUR][1000 genomes]
rs9997027	1.00[CEU][hapmap];0.95[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9999321	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1028958	chr4:148377752-148793485	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
2	nsv498083	chr4:148519825-148917583	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	nsv880243	chr4:148735644-148879583	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv880244	chr4:148764252-148920089	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
5	nsv1029845	chr4:148766290-148916437	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
6	nsv1030001	chr4:148773479-148916437	Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:148763200-148796200	Weak transcription	Monocytes-CD14+_RO01746	blood
2	chr4:148766600-148796200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr4:148767600-148796400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr4:148768400-148815600	Weak transcription	Primary T cells from cord blood	blood
5	chr4:148770400-148796200	Weak transcription	Fetal Kidney	kidney
6	chr4:148772000-148806000	Weak transcription	Fetal Thymus	thymus
7	chr4:148777000-148796200	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr4:148777000-148823000	Weak transcription	Small Intestine	intestine
9	chr4:148777400-148796600	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:148777800-148796200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr4:148779800-148793800	Weak transcription	Fetal Lung	lung
12	chr4:148782000-148799400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr4:148783000-148796200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
14	chr4:148783000-148796200	Weak transcription	Thymus	Thymus
15	chr4:148783400-148796400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr4:148783400-148796400	Weak transcription	Lung	lung
17	chr4:148783600-148789800	Weak transcription	Fetal Intestine Small	intestine
18	chr4:148783600-148796200	Weak transcription	Esophagus	oesophagus
19	chr4:148783600-148796200	Weak transcription	Placenta	Placenta
20	chr4:148783800-148789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr4:148783800-148790000	Weak transcription	Left Ventricle	heart
22	chr4:148783800-148796200	Weak transcription	Fetal Intestine Large	intestine
23	chr4:148783800-148796200	Weak transcription	Gastric	stomach
24	chr4:148783800-148796200	Weak transcription	Right Ventricle	heart
25	chr4:148784400-148810800	Weak transcription	Fetal Heart	heart
26	chr4:148784600-148796400	Weak transcription	Duodenum Mucosa	Duodenum
27	chr4:148785400-148796200	Weak transcription	GM12878-XiMat	blood
28	chr4:148785600-148796200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr4:148786000-148789800	Weak transcription	Skeletal Muscle Female	skeletal muscle
30	chr4:148786000-148790200	Strong transcription	HSMM	muscle
31	chr4:148786000-148804000	Weak transcription	Psoas Muscle	Psoas
32	chr4:148786000-148861400	Weak transcription	Pancreas	Pancrea
33	chr4:148786400-148796200	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr4:148787000-148789400	Weak transcription	Duodenum Smooth Muscle	Duodenum
35	chr4:148787000-148794000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr4:148787200-148790400	Strong transcription	Fetal Muscle Trunk	muscle
37	chr4:148787400-148789400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr4:148787400-148789400	Weak transcription	Ovary	ovary
39	chr4:148787400-148789600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr4:148787400-148789800	Strong transcription	Muscle Satellite Cultured Cells	--
41	chr4:148787400-148795600	Weak transcription	NH-A	brain
42	chr4:148787400-148796200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr4:148787400-148800400	Weak transcription	NHEK	skin
44	chr4:148787600-148796200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr4:148787600-148796200	Weak transcription	Osteobl	bone
46	chr4:148787600-148801600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
47	chr4:148787800-148790000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr4:148787800-148790400	Strong transcription	HSMMtube	muscle
49	chr4:148787800-148791000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr4:148787800-148793600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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