Variant report

Variant	rs12571756
Chromosome Location	chr10:112758123-112758124
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr10:112746021..112748310-chr10:112757696..112760493,2	MCF-7	breast:

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs11195405	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11195417	0.94[JPT][hapmap]
rs11195419	0.94[JPT][hapmap]
rs11592715	0.92[ASN][1000 genomes]
rs11599619	0.92[ASN][1000 genomes]
rs12569835	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12572049	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17128130	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17128212	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128356	0.86[CEU][hapmap];0.94[JPT][hapmap];0.86[YRI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2295992	0.81[ASN][1000 genomes]
rs3750625	0.94[JPT][hapmap];0.86[YRI][hapmap]
rs4391757	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55794717	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56233990	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56784382	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs56946887	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58164562	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7072811	0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7073594	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7073880	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73343848	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73343859	0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73343879	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73345956	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs74156313	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7902347	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035602	chr10:112636053-112781413	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1051327	chr10:112650316-112772917	ZNF genes & repeats Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS 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	27 gene(s)	inside rSNPs	diseases
3	nsv540774	chr10:112650316-112772917	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv831985	chr10:112652089-112803103	Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
5	nsv1048809	chr10:112683822-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1042020	chr10:112686323-112795159	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
7	nsv1035422	chr10:112724159-112764594	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region miRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1048444	chr10:112724159-112795159	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv1036202	chr10:112726834-112781413	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv1051595	chr10:112730022-112789048	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
11	nsv1047412	chr10:112747749-112781413	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12571756	SHOC2	cis	multi-tissue	Pritchard

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:112700600-112764000	Weak transcription	Placenta	Placenta
2	chr10:112705200-112789800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr10:112707200-112784200	Weak transcription	Left Ventricle	heart
4	chr10:112709000-112760000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr10:112719400-112760800	Weak transcription	Fetal Muscle Leg	muscle
6	chr10:112719800-112759200	Weak transcription	Fetal Lung	lung
7	chr10:112723200-112783000	Weak transcription	Small Intestine	intestine
8	chr10:112724800-112760200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr10:112726600-112764000	Weak transcription	HUVEC	blood vessel
10	chr10:112727400-112764400	Weak transcription	Adipose Nuclei	Adipose
11	chr10:112732400-112763800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr10:112732600-112789400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr10:112732800-112782800	Weak transcription	Esophagus	oesophagus
14	chr10:112732800-112789400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr10:112738000-112782800	Weak transcription	Rectal Smooth Muscle	rectum
16	chr10:112738200-112784600	Weak transcription	Ovary	ovary
17	chr10:112738400-112779400	Weak transcription	HepG2	liver
18	chr10:112739200-112774400	Weak transcription	Gastric	stomach
19	chr10:112739400-112764400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
20	chr10:112739600-112769000	Weak transcription	Fetal Kidney	kidney
21	chr10:112740400-112791800	Weak transcription	Colon Smooth Muscle	Colon
22	chr10:112740600-112761000	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr10:112744800-112778800	Weak transcription	Hela-S3	cervix
24	chr10:112745600-112762400	Weak transcription	Duodenum Mucosa	Duodenum
25	chr10:112745600-112769400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr10:112745600-112777600	Weak transcription	Pancreas	Pancrea
27	chr10:112746000-112758200	Weak transcription	Stomach Mucosa	stomach
28	chr10:112746000-112783400	Weak transcription	Colonic Mucosa	Colon
29	chr10:112746800-112763800	Weak transcription	Fetal Stomach	stomach
30	chr10:112746800-112782800	Weak transcription	Psoas Muscle	Psoas
31	chr10:112747000-112760600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr10:112747400-112758600	Weak transcription	Liver	Liver
33	chr10:112747400-112779800	Weak transcription	Fetal Brain Male	brain
34	chr10:112747600-112785200	Weak transcription	Fetal Brain Female	brain
35	chr10:112749000-112760200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr10:112749200-112789400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr10:112749800-112758200	Weak transcription	Primary B cells from peripheral blood	blood
38	chr10:112750400-112785000	Weak transcription	A549	lung
39	chr10:112751800-112772600	Weak transcription	K562	blood
40	chr10:112752000-112764200	Weak transcription	Duodenum Smooth Muscle	Duodenum
41	chr10:112752200-112760000	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr10:112752400-112760000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr10:112752800-112763600	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr10:112753000-112764000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr10:112753000-112772600	Weak transcription	Brain Angular Gyrus	brain
46	chr10:112753200-112761000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr10:112753200-112764600	Weak transcription	Thymus	Thymus
48	chr10:112753200-112779200	Weak transcription	Brain Hippocampus Middle	brain
49	chr10:112753200-112779600	Weak transcription	Brain Anterior Caudate	brain
50	chr10:112753200-112782600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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