Variant report

Variant	rs17036489
Chromosome Location	chr12:105292284-105292285
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105290364..105293204-chr12:105349716..105351702,2	MCF-7	breast:

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1048662	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs10778350	0.86[EUR][1000 genomes]
rs11112189	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11834087	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12307301	0.86[EUR][1000 genomes]
rs12320887	0.86[EUR][1000 genomes]
rs12321404	0.86[EUR][1000 genomes]
rs12579120	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12579129	0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12579202	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12579441	0.93[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12579469	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12579505	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs12579790	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12579945	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12580114	1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12580128	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12580384	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs12580794	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12582090	0.86[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap]
rs12582312	0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17036358	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17036429	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17036433	0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17036545	0.93[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs17036606	1.00[GIH][hapmap];1.00[JPT][hapmap]
rs4369494	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4545639	0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs57144501	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs57685442	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs59079144	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs60976244	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61129422	0.93[ASN][1000 genomes]
rs61262317	0.86[EUR][1000 genomes]
rs61587191	0.86[EUR][1000 genomes]
rs7302213	0.86[EUR][1000 genomes]
rs73383408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73383420	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73383435	1.00[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73383439	1.00[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs73383441	0.92[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs73383467	0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs73383473	0.91[ASN][1000 genomes]
rs73394174	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs73394185	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73394186	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73396157	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73396159	1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73399912	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73399925	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73399927	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73399929	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73399931	1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73399934	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73399944	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73399947	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73399956	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73399960	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73399968	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971315	0.86[EUR][1000 genomes]
rs7971613	0.86[EUR][1000 genomes]
rs7972699	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7976092	0.90[ASN][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	nsv899495	chr12:104990469-105527011	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv899498	chr12:105173598-105461620	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17036489	KCNA1	trans	brain	seeQTL
rs17036489	ROR1	trans	brain	seeQTL
rs17036489	TSPAN18	trans	brain	seeQTL
rs17036489	COMP	trans	brain	seeQTL
rs17036489	EPS8L2	trans	brain	seeQTL
rs17036489	CLEC4G	trans	brain	seeQTL
rs17036489	PKIB	trans	brain	seeQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105275400-105297000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr12:105278400-105293200	Weak transcription	Duodenum Mucosa	Duodenum
3	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr12:105284600-105309000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr12:105285000-105296200	Weak transcription	Aorta	Aorta
6	chr12:105290400-105292600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:105290600-105297200	Weak transcription	HepG2	liver
8	chr12:105290800-105295600	Weak transcription	Stomach Mucosa	stomach
9	chr12:105290800-105296400	Weak transcription	Pancreas	Pancrea
10	chr12:105290800-105331600	Weak transcription	Gastric	stomach
11	chr12:105291000-105292600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:105291800-105294400	Weak transcription	Liver	Liver
13	chr12:105292000-105297600	Weak transcription	Colon Smooth Muscle	Colon

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