Variant report

Variant	rs10507185
Chromosome Location	chr12:105290200-105290201
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:105277401..105280097-chr12:105289750..105292051,2	MCF-7	breast:
2	chr12:105289655..105291456-chr12:105306403..105308670,2	MCF-7	breast:
3	chr12:105289003..105291850-chr12:105292916..105295030,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10507183	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.89[ASN][1000 genomes]
rs10778354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778356	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861278	0.88[ASN][1000 genomes]
rs10861280	0.85[ASN][1000 genomes]
rs10861282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10861291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861293	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861295	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861297	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11112208	0.94[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs11112221	0.92[ASN][1000 genomes]
rs11112234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12230637	0.94[CHB][hapmap];0.97[CHD][hapmap];0.88[JPT][hapmap];0.94[ASN][1000 genomes]
rs17829927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2047126	0.87[ASN][1000 genomes]
rs2245695	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2249941	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2252843	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2264883	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2264893	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2453163	0.89[ASN][1000 genomes]
rs2453164	0.89[ASN][1000 genomes]
rs2453169	0.93[CHB][hapmap];0.87[ASN][1000 genomes]
rs2463430	0.84[ASN][1000 genomes]
rs2468088	0.83[ASN][1000 genomes]
rs2468094	0.85[ASN][1000 genomes]
rs2468096	0.88[ASN][1000 genomes]
rs2468098	0.88[ASN][1000 genomes]
rs2468103	0.89[ASN][1000 genomes]
rs2468107	0.94[CHB][hapmap];0.86[JPT][hapmap];0.89[ASN][1000 genomes]
rs2468108	0.89[ASN][1000 genomes]
rs2468336	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2468338	0.94[CHB][hapmap];0.82[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468339	0.94[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468341	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs2468342	0.85[ASN][1000 genomes]
rs2468343	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.89[ASN][1000 genomes]
rs2468344	0.83[ASN][1000 genomes]
rs2468345	0.85[ASN][1000 genomes]
rs2468396	0.92[EUR][1000 genomes]
rs2468397	0.86[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2642119	0.89[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2730294	0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs3890816	0.84[CEU][hapmap]
rs4130161	0.87[CHB][hapmap];0.87[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4257060	0.89[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4537841	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4630370	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.81[MKK][hapmap];0.91[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4644704	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4964116	0.88[CEU][hapmap]
rs7959777	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7961766	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7971260	0.89[ASN][1000 genomes]
rs7971392	0.91[ASN][1000 genomes]
rs9705471	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10507185	C12orf42	cis	cerebellum	SCAN
rs10507185	GNPTAB	cis	parietal	SCAN

Chromatin state (count:14 , 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	chr12:105285000-105290400	Weak transcription	Gastric	stomach
6	chr12:105285000-105296200	Weak transcription	Aorta	Aorta
7	chr12:105289000-105290400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
8	chr12:105289000-105290600	Enhancers	Pancreatic Islets	Pancreatic Islet
9	chr12:105289000-105290600	Enhancers	Hela-S3	cervix
10	chr12:105289000-105290600	Enhancers	HepG2	liver
11	chr12:105289400-105290200	Flanking Active TSS	A549	lung
12	chr12:105289800-105290800	Flanking Active TSS	Liver	Liver
13	chr12:105289800-105290800	Enhancers	Stomach Mucosa	stomach
14	chr12:105290200-105290800	Enhancers	A549	lung

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