Variant report

Variant	rs7956101
Chromosome Location	chr12:62724863-62724864
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62724788..62726773-chr12:62756335..62758286,2	MCF-7	breast:
2	chr12:62724789..62726795-chr12:62726808..62728651,2	K562	blood:
3	chr12:62720361..62722698-chr12:62723343..62725405,2	MCF-7	breast:
4	chr12:62717168..62719794-chr12:62722542..62725055,3	K562	blood:

Variant related genes	Relation type
ENSG00000200814	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1032417	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10431566	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10732749	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784290	1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10784291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10877825	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11174432	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1376341	0.81[CEU][hapmap]
rs1512024	1.00[CEU][hapmap];0.97[GIH][hapmap];0.83[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1901238	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2122659	1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2131436	0.85[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2131437	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167286	0.93[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4763167	0.80[CEU][hapmap]
rs7135737	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7312416	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7312513	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7315790	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7953445	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	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7974980	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[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	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
4	nsv530690	chr12:62678463-62999462	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	54 gene(s)	inside rSNPs	diseases
5	nsv899153	chr12:62716330-62817736	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7956101	R3HDM2	cis	cerebellum	SCAN
rs7956101	LRP1	cis	parietal	SCAN
rs7956101	OS9	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:62686400-62736400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr12:62691200-62736400	Weak transcription	Esophagus	oesophagus
3	chr12:62691200-62736600	Weak transcription	Lung	lung
4	chr12:62698400-62741800	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr12:62698600-62725800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr12:62698600-62745800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:62698800-62728600	Weak transcription	Fetal Heart	heart
8	chr12:62699800-62736400	Weak transcription	Aorta	Aorta
9	chr12:62700000-62726600	Weak transcription	HSMMtube	muscle
10	chr12:62700000-62736400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr12:62700000-62736400	Weak transcription	Fetal Stomach	stomach
12	chr12:62700000-62737000	Weak transcription	NHLF	lung
13	chr12:62700000-62757000	Weak transcription	HUVEC	blood vessel
14	chr12:62701600-62730800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr12:62701600-62738600	Weak transcription	Fetal Brain Male	brain
16	chr12:62701600-62742000	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr12:62701600-62769200	Weak transcription	NHEK	skin
18	chr12:62710000-62744400	Weak transcription	Pancreas	Pancrea
19	chr12:62712200-62755400	Weak transcription	Small Intestine	intestine
20	chr12:62713000-62732400	Weak transcription	Fetal Muscle Leg	muscle
21	chr12:62713200-62736400	Weak transcription	Gastric	stomach
22	chr12:62714200-62736400	Weak transcription	Spleen	Spleen
23	chr12:62716200-62736400	Weak transcription	Ovary	ovary
24	chr12:62716800-62726000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr12:62716800-62729800	Weak transcription	Psoas Muscle	Psoas
26	chr12:62716800-62736000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr12:62716800-62736000	Weak transcription	Thymus	Thymus
28	chr12:62716800-62736200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr12:62716800-62736200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr12:62716800-62736400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr12:62716800-62736400	Weak transcription	Colonic Mucosa	Colon
32	chr12:62716800-62736400	Weak transcription	Fetal Muscle Trunk	muscle
33	chr12:62716800-62736600	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr12:62717000-62725600	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr12:62717000-62726600	Weak transcription	GM12878-XiMat	blood
36	chr12:62717000-62728600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr12:62717000-62731000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
38	chr12:62717000-62732400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr12:62717000-62736400	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr12:62717000-62736600	Weak transcription	Duodenum Mucosa	Duodenum
41	chr12:62717000-62736600	Weak transcription	Rectal Smooth Muscle	rectum
42	chr12:62717000-62736800	Weak transcription	Fetal Lung	lung
43	chr12:62717000-62737000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr12:62717000-62737400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
45	chr12:62717000-62750200	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr12:62717000-62769200	Weak transcription	Fetal Kidney	kidney
47	chr12:62717000-62777000	Weak transcription	Duodenum Smooth Muscle	Duodenum
48	chr12:62717000-62783200	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr12:62717000-62784600	Weak transcription	Colon Smooth Muscle	Colon
50	chr12:62717200-62725200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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