Variant report

Variant	rs10843505
Chromosome Location	chr12:29929483-29929484
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:29926045..29928762-chr12:29929311..29931905,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs11050423	0.89[MEX][hapmap];0.92[AMR][1000 genomes]
rs11050426	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11050429	0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11050430	1.00[ASW][hapmap];0.93[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.88[JPT][hapmap];1.00[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs11050431	0.87[ASN][1000 genomes]
rs11050433	0.86[ASN][1000 genomes]
rs11050436	1.00[AFR][1000 genomes]
rs12370447	0.86[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs16934870	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.92[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2126891	1.00[ASW][hapmap]
rs36100969	0.86[ASN][1000 genomes]
rs60952280	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73077434	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs73079425	1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529328	chr12:29692414-30246209	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv898953	chr12:29905322-29989292	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10843505	OVCH1	cis	parietal	SCAN
rs10843505	CCDC91	cis	parietal	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29916000-29931400	Weak transcription	Pancreas	Pancrea
2	chr12:29921600-29934000	Weak transcription	Fetal Kidney	kidney
3	chr12:29922600-29929600	Weak transcription	HSMM	muscle
4	chr12:29922600-29931000	Weak transcription	Colon Smooth Muscle	Colon
5	chr12:29922600-29931800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr12:29922600-29934000	Weak transcription	NHLF	lung
7	chr12:29922800-29930600	Weak transcription	Stomach Smooth Muscle	stomach
8	chr12:29922800-29931200	Weak transcription	Aorta	Aorta
9	chr12:29922800-29933800	Weak transcription	Hela-S3	cervix
10	chr12:29924600-29931600	Weak transcription	Adipose Nuclei	Adipose
11	chr12:29925400-29934000	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr12:29925600-29934200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr12:29926400-29931400	Weak transcription	Ovary	ovary
14	chr12:29926400-29931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:29926600-29931400	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:29927000-29929600	Weak transcription	Left Ventricle	heart
17	chr12:29927000-29930800	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr12:29927000-29931400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr12:29927200-29931400	Weak transcription	Fetal Heart	heart
20	chr12:29927200-29931800	Weak transcription	Right Atrium	heart
21	chr12:29927200-29931800	Weak transcription	Right Ventricle	heart
22	chr12:29927200-29931800	Weak transcription	Spleen	Spleen
23	chr12:29927400-29930000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr12:29927600-29929800	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
25	chr12:29927600-29929800	Strong transcription	Muscle Satellite Cultured Cells	--
26	chr12:29927800-29929800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:29927800-29931000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr12:29928200-29930000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr12:29928200-29930000	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
30	chr12:29928400-29929600	Weak transcription	Psoas Muscle	Psoas
31	chr12:29928800-29934800	Weak transcription	Fetal Muscle Trunk	muscle
32	chr12:29929000-29930800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr12:29929200-29931800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr12:29929200-29931800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr12:29929200-29931800	Weak transcription	Fetal Muscle Leg	muscle
36	chr12:29929200-29932400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:29929400-29932800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr12:29929400-29932800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr12:29929400-29933200	Weak transcription	HMEC	breast

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