Variant report

Variant	rs11175189
Chromosome Location	chr12:64246075-64246076
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:64243148..64249002-chr12:64249405..64253780,7	MCF-7	breast:
2	chr12:64235116..64240404-chr12:64242494..64248805,7	MCF-7	breast:
3	chr12:64237577..64240346-chr12:64245227..64250030,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000196935	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11175184	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11175185	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11175188	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11175197	0.96[ASN][1000 genomes]
rs11833808	0.85[CEU][hapmap];0.86[CHB][hapmap];0.90[JPT][hapmap];0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11835034	0.94[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12228199	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12229790	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12579795	0.89[YRI][hapmap];0.81[EUR][1000 genomes]
rs17099866	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2335884	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35143986	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4072758	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55642517	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55655348	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55760535	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55907605	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55930806	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56028204	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56080061	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56264182	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58424013	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59063572	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60031756	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6581509	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581510	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66856673	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67401817	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67684483	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs67830727	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs67880496	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67892056	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs67993208	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs68188132	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7136130	1.00[ASW][hapmap];0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7294327	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7301437	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7302672	0.83[CEU][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304340	1.00[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7305893	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7307108	0.83[CEU][hapmap];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7308850	0.89[ASW][hapmap];0.88[MEX][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310327	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7310329	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7310575	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7311611	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73313479	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73315321	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73315365	0.98[ASN][1000 genomes]
rs7953208	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]

Variant overlapped rSNPs/rCNVs (count:9 , 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	esv2759905	chr12:63901801-64252172	Bivalent Enhancer Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	esv2758312	chr12:63910416-64252172	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
4	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
5	nsv832441	chr12:64063776-64252172	Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	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
7	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
8	esv1797043	chr12:64237504-64256568	Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Enhancers Weak transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
9	esv1833454	chr12:64237504-64264837	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	10 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11175189	SRGAP1	cis	cerebellum	SCAN

Chromatin state (count:52 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:64240400-64247400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
2	chr12:64240800-64256000	Weak transcription	Small Intestine	intestine
3	chr12:64241000-64247000	Weak transcription	HepG2	liver
4	chr12:64241000-64247400	Weak transcription	Ovary	ovary
5	chr12:64241000-64251800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr12:64241000-64255600	Weak transcription	Left Ventricle	heart
7	chr12:64241000-64256000	Weak transcription	Fetal Muscle Leg	muscle
8	chr12:64241000-64256000	Weak transcription	HSMM	muscle
9	chr12:64241000-64257200	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr12:64241000-64261200	Weak transcription	Fetal Muscle Trunk	muscle
11	chr12:64241000-64268800	Weak transcription	Lung	lung
12	chr12:64241000-64278800	Weak transcription	Fetal Stomach	stomach
13	chr12:64243000-64251200	Weak transcription	NHLF	lung
14	chr12:64243400-64247800	Enhancers	Fetal Brain Male	brain
15	chr12:64243400-64263000	Weak transcription	NHEK	skin
16	chr12:64243600-64256200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr12:64243800-64251400	Weak transcription	Osteobl	bone
18	chr12:64244000-64247200	Weak transcription	Fetal Kidney	kidney
19	chr12:64244000-64247400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:64244000-64247400	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr12:64244000-64250200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr12:64244000-64250200	Weak transcription	NHDF-Ad	bronchial
23	chr12:64244000-64250400	Weak transcription	Hela-S3	cervix
24	chr12:64244000-64251600	Weak transcription	HMEC	breast
25	chr12:64244000-64256000	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr12:64244000-64263600	Weak transcription	Fetal Lung	lung
27	chr12:64244200-64246200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:64244200-64250600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr12:64244200-64251400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr12:64244200-64251600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:64244400-64247400	Weak transcription	Brain Substantia Nigra	brain
32	chr12:64244400-64247800	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:64244400-64251200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:64244400-64256000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr12:64244600-64246400	Weak transcription	Fetal Intestine Large	intestine
36	chr12:64244600-64251200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:64244800-64255800	Weak transcription	Brain Anterior Caudate	brain
38	chr12:64245400-64246200	Strong transcription	Fetal Intestine Small	intestine
39	chr12:64245600-64246200	Enhancers	HUES48 Cell Line	embryonic stem cell
40	chr12:64245600-64246200	Enhancers	Fetal Brain Female	brain
41	chr12:64245600-64246400	Enhancers	Brain Germinal Matrix	brain
42	chr12:64245800-64246200	Enhancers	Pancreas	Pancrea
43	chr12:64245800-64246400	Enhancers	HUES64 Cell Line	embryonic stem cell
44	chr12:64245800-64246600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
45	chr12:64246000-64246200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr12:64246000-64246200	Enhancers	Brain Cingulate Gyrus	brain
47	chr12:64246000-64246400	Enhancers	iPS-18 Cell Line	embryonic stem cell
48	chr12:64246000-64246400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:64246000-64246400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr12:64246000-64246600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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