Variant report

Variant	rs7953208
Chromosome Location	chr12:64268005-64268006
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:64265884..64268355-chr12:64269681..64272144,3	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11175184	0.94[ASN][1000 genomes]
rs11175185	0.94[ASN][1000 genomes]
rs11175188	0.97[ASN][1000 genomes]
rs11175189	0.84[ASW][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.97[ASN][1000 genomes]
rs11175197	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11833808	0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs11835034	0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.97[ASN][1000 genomes]
rs12228199	0.84[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs12229790	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs17099866	0.87[ASN][1000 genomes]
rs2335884	0.97[ASN][1000 genomes]
rs35143986	0.84[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.90[TSI][hapmap];0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4072758	0.83[ASN][1000 genomes]
rs55642517	0.97[ASN][1000 genomes]
rs55655348	0.83[ASN][1000 genomes]
rs55760535	0.87[ASN][1000 genomes]
rs55907605	0.97[ASN][1000 genomes]
rs55930806	0.83[ASN][1000 genomes]
rs56028204	0.97[ASN][1000 genomes]
rs56080061	0.97[ASN][1000 genomes]
rs56264182	0.87[ASN][1000 genomes]
rs58424013	0.97[ASN][1000 genomes]
rs60031756	0.87[ASN][1000 genomes]
rs6581509	0.97[ASN][1000 genomes]
rs6581510	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs66856673	0.97[ASN][1000 genomes]
rs67401817	0.97[ASN][1000 genomes]
rs67684483	0.87[ASN][1000 genomes]
rs67830727	0.97[ASN][1000 genomes]
rs67880496	0.97[ASN][1000 genomes]
rs67892056	0.96[ASN][1000 genomes]
rs67993208	0.97[ASN][1000 genomes]
rs68188132	0.87[ASN][1000 genomes]
rs7136130	0.84[ASW][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.87[ASN][1000 genomes]
rs7294327	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs7301437	0.80[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7302672	0.84[ASN][1000 genomes]
rs7304340	0.84[ASW][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.97[ASN][1000 genomes]
rs7305893	0.85[ASN][1000 genomes]
rs7307108	0.83[ASN][1000 genomes]
rs7308850	0.83[ASW][hapmap];0.87[CHB][hapmap];0.83[ASN][1000 genomes]
rs7310327	0.84[ASW][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.88[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs7310329	0.83[ASN][1000 genomes]
rs7310575	0.97[ASN][1000 genomes]
rs7311611	0.83[ASN][1000 genomes]
rs73313479	0.87[ASN][1000 genomes]
rs73315321	0.96[ASN][1000 genomes]
rs73315365	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[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	nsv1046836	chr12:63392391-64377169	Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
2	esv2751110	chr12:63939733-64274680	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv832442	chr12:64228071-64442771	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	esv1810729	chr12:64234926-64268005	Active TSS Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
5	nsv975506	chr12:64265506-64268351	Weak transcription ZNF genes & repeats Enhancers Genic enhancers	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7953208	LLPH	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64241000-64268800	Weak transcription	Lung	lung
2	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
3	chr12:64246200-64286400	Weak transcription	Fetal Brain Female	brain
4	chr12:64247800-64268200	Weak transcription	Fetal Brain Male	brain
5	chr12:64250200-64287200	Weak transcription	Aorta	Aorta
6	chr12:64256800-64271400	Weak transcription	Brain Angular Gyrus	brain
7	chr12:64256800-64276600	Weak transcription	HSMM	muscle
8	chr12:64256800-64282600	Weak transcription	Gastric	stomach
9	chr12:64257400-64270600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr12:64258800-64286200	Weak transcription	Fetal Intestine Small	intestine
11	chr12:64261200-64268800	Weak transcription	Stomach Mucosa	stomach
12	chr12:64263200-64270800	Weak transcription	Pancreas	Pancrea
13	chr12:64263600-64269000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr12:64263600-64278800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr12:64263800-64268800	Weak transcription	NHDF-Ad	bronchial
16	chr12:64263800-64276600	Weak transcription	NHLF	lung
17	chr12:64263800-64289200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:64264000-64268800	Weak transcription	Fetal Lung	lung
19	chr12:64264000-64271600	Weak transcription	Osteobl	bone
20	chr12:64264000-64276600	Weak transcription	HSMMtube	muscle
21	chr12:64264000-64279000	Weak transcription	NHEK	skin
22	chr12:64264000-64282600	Weak transcription	HMEC	breast
23	chr12:64264000-64294400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:64264200-64270200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr12:64264200-64271600	Weak transcription	Hela-S3	cervix
26	chr12:64264200-64282400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr12:64264600-64269200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr12:64265200-64269000	Weak transcription	Ovary	ovary
29	chr12:64266600-64268800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:64266800-64269000	Weak transcription	A549	lung
31	chr12:64266800-64270800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr12:64267000-64271800	Weak transcription	Fetal Heart	heart
33	chr12:64267600-64268200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr12:64267600-64268800	Weak transcription	Esophagus	oesophagus
35	chr12:64267800-64269200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr12:64267800-64271200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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