Variant report

Variant	rs7953445
Chromosome Location	chr12:62664657-62664658
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62654217..62657046-chr12:62663377..62665322,2	MCF-7	breast:
2	chr12:62652480..62656842-chr12:62660484..62666206,11	MCF-7	breast:
3	chr12:62663412..62666237-chr12:62669959..62672876,3	K562	blood:

Variant related genes	Relation type
ENSG00000198673	Chromatin interaction
ENSG00000135655	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1032417	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10431566	0.92[AMR][1000 genomes]
rs10732749	0.94[AMR][1000 genomes]
rs10784290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10784291	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10877825	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11174432	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1376341	0.81[CEU][hapmap]
rs1512024	1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1901238	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2122659	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2131436	0.83[ASN][1000 genomes]
rs2131437	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2167286	0.82[CHB][hapmap];0.94[JPT][hapmap];0.94[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4763167	0.80[CEU][hapmap]
rs7135737	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7312416	0.97[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7312513	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7315790	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7956101	1.00[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7970898	0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7974980	1.00[CEU][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035150	chr12:62615347-62785005	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1049465	chr12:62657011-62785005	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
3	nsv1053403	chr12:62657011-62809413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7953445	LRP1	cis	parietal	SCAN
rs7953445	R3HDM2	cis	cerebellum	SCAN
rs7953445	OS9	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62655400-62685600	Weak transcription	HSMM	muscle
2	chr12:62656000-62664800	Weak transcription	Fetal Stomach	stomach
3	chr12:62656000-62665400	Weak transcription	Brain Angular Gyrus	brain
4	chr12:62656000-62668200	Weak transcription	Right Atrium	heart
5	chr12:62656400-62669600	Enhancers	Liver	Liver
6	chr12:62656400-62679400	Weak transcription	Brain Anterior Caudate	brain
7	chr12:62656600-62668400	Weak transcription	Fetal Brain Female	brain
8	chr12:62656600-62685600	Weak transcription	Aorta	Aorta
9	chr12:62656600-62685600	Weak transcription	Pancreas	Pancrea
10	chr12:62656800-62675400	Weak transcription	Brain Hippocampus Middle	brain
11	chr12:62657400-62666600	Weak transcription	HepG2	liver
12	chr12:62658400-62669400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr12:62658400-62671200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr12:62658400-62671400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:62659000-62671800	Enhancers	Primary T helper cells fromperipheralblood	blood
16	chr12:62659200-62669800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr12:62659400-62671400	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr12:62659600-62667800	Weak transcription	Left Ventricle	heart
19	chr12:62660800-62665000	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr12:62661000-62664800	Enhancers	Hela-S3	cervix
21	chr12:62661200-62665000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
22	chr12:62661400-62673600	Weak transcription	Brain Cingulate Gyrus	brain
23	chr12:62661600-62665400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr12:62661600-62667800	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr12:62661600-62668600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
26	chr12:62661600-62676000	Weak transcription	Fetal Thymus	thymus
27	chr12:62661600-62682800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr12:62661800-62666800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr12:62662200-62676000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr12:62662400-62666600	Weak transcription	NHLF	lung
31	chr12:62662600-62666800	Weak transcription	Primary B cells from peripheral blood	blood
32	chr12:62662800-62669600	Weak transcription	Duodenum Mucosa	Duodenum
33	chr12:62663000-62666400	Weak transcription	A549	lung
34	chr12:62663000-62668200	Weak transcription	Skeletal Muscle Female	skeletal muscle
35	chr12:62663000-62685600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr12:62663200-62665600	Enhancers	Dnd41	blood
37	chr12:62663200-62669400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr12:62663200-62670800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr12:62663200-62671600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr12:62663200-62684800	Weak transcription	NHEK	skin
41	chr12:62663400-62667400	Weak transcription	Osteobl	bone
42	chr12:62663400-62667800	Weak transcription	Small Intestine	intestine
43	chr12:62663400-62685600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr12:62663600-62664800	Enhancers	Primary hematopoietic stem cells	blood
45	chr12:62663600-62666600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:62663600-62666800	Weak transcription	Thymus	Thymus
47	chr12:62663600-62667800	Weak transcription	Primary T cells fromperipheralblood	blood
48	chr12:62663600-62667800	Weak transcription	Psoas Muscle	Psoas
49	chr12:62663600-62668000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
50	chr12:62663600-62668200	Weak transcription	Ovary	ovary

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