Variant report

Variant	rs6484785
Chromosome Location	chr11:35381907-35381908
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:35373926..35376824-chr11:35378507..35382009,3	MCF-7	breast:
2	chr11:35325349..35327206-chr11:35381816..35384283,2	MCF-7	breast:
3	chr11:35342453..35346425-chr11:35381907..35387258,7	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1042113	0.84[JPT][hapmap]
rs11033064	0.81[JPT][hapmap]
rs11033071	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs11033080	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[TSI][hapmap];0.90[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11033083	0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs11033089	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11033090	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12420201	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12574069	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs16927292	0.83[CHB][hapmap]
rs2273687	0.83[ASN][1000 genomes]
rs2901534	0.90[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3794087	0.81[CEU][hapmap];0.83[CHB][hapmap]
rs3847612	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.84[ASN][1000 genomes]
rs3847613	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3847620	0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3891872	0.83[CHB][hapmap]
rs3911898	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs3925877	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4083481	0.86[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs4237664	0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs4582949	0.89[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4755397	0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4755398	0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756207	0.83[CHB][hapmap]
rs4756210	0.83[ASN][1000 genomes]
rs4756211	0.86[CEU][hapmap];0.91[CHB][hapmap];0.89[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[TSI][hapmap];0.85[ASN][1000 genomes]
rs4756219	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4756220	0.88[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4756221	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs4756222	0.81[JPT][hapmap]
rs55709010	0.84[ASN][1000 genomes]
rs7114383	0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.89[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs72076042	0.80[ASN][1000 genomes]
rs7934047	0.89[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes];0.91[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	nsv1045837	chr11:34893992-35395190	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv832120	chr11:35277410-35490304	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	esv2758264	chr11:35319320-35480522	Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	esv2759819	chr11:35319320-35480522	Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv430372	chr11:35376124-35430324	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6484785	GOLGA1	trans	brain	seeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:35367000-35385400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr11:35370200-35384200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr11:35374400-35384600	Weak transcription	Psoas Muscle	Psoas
4	chr11:35374400-35384600	Weak transcription	Right Ventricle	heart
5	chr11:35375000-35383600	Weak transcription	Left Ventricle	heart
6	chr11:35376400-35384400	Weak transcription	Skeletal Muscle Female	skeletal muscle
7	chr11:35376600-35385000	Weak transcription	HSMM	muscle
8	chr11:35377000-35383800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:35377000-35384600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr11:35377000-35384600	Weak transcription	Right Atrium	heart
11	chr11:35377200-35384400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr11:35377200-35384800	Weak transcription	Osteobl	bone
13	chr11:35379000-35382000	Enhancers	Hela-S3	cervix
14	chr11:35379200-35382000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr11:35379400-35382200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr11:35379400-35382400	Enhancers	NHDF-Ad	bronchial
17	chr11:35379800-35382200	Enhancers	Adipose Nuclei	Adipose
18	chr11:35379800-35382200	Enhancers	Brain Anterior Caudate	brain
19	chr11:35379800-35384600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr11:35380200-35382200	Flanking Active TSS	Liver	Liver
21	chr11:35380400-35382000	Enhancers	Brain Hippocampus Middle	brain
22	chr11:35380400-35382200	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr11:35380400-35382200	Enhancers	Colon Smooth Muscle	Colon
24	chr11:35380400-35384800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:35380600-35383600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr11:35380800-35382000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr11:35380800-35382000	Enhancers	Brain Substantia Nigra	brain
28	chr11:35381000-35382200	Enhancers	Breast Myoepithelial Primary Cells	Breast
29	chr11:35381000-35384600	Weak transcription	Aorta	Aorta
30	chr11:35381200-35382000	Enhancers	Fetal Muscle Leg	muscle
31	chr11:35381200-35384600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr11:35381400-35382000	Enhancers	Fetal Brain Female	brain
33	chr11:35381400-35382200	Enhancers	Brain Angular Gyrus	brain
34	chr11:35381400-35382200	Enhancers	Brain Cingulate Gyrus	brain
35	chr11:35381400-35384600	Weak transcription	Esophagus	oesophagus
36	chr11:35381600-35382000	Enhancers	Pancreas	Pancrea
37	chr11:35381600-35382000	Enhancers	HSMMtube	muscle
38	chr11:35381600-35382200	Enhancers	Stomach Smooth Muscle	stomach
39	chr11:35381600-35382800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
40	chr11:35381600-35384600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr11:35381800-35382000	Bivalent Enhancer	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr11:35381800-35382000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr11:35381800-35382000	Enhancers	Fetal Heart	heart
44	chr11:35381800-35382200	Enhancers	HepG2	liver
45	chr11:35381800-35382400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr11:35381800-35384400	Weak transcription	Rectal Smooth Muscle	rectum
47	chr11:35381800-35384400	Weak transcription	NHLF	lung
48	chr11:35381800-35384800	Weak transcription	HMEC	breast
49	chr11:35381800-35385400	Weak transcription	Fetal Brain Male	brain

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