Variant report

Variant	rs7959777
Chromosome Location	chr12:105306997-105306998
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:105289655..105291456-chr12:105306403..105308670,2	MCF-7	breast:
2	chr12:105294762..105296440-chr12:105304939..105307469,2	K562	blood:

Extended variants
information (count: 63 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10507183	0.94[CHB][hapmap];0.90[CHD][hapmap];0.81[GIH][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs10507185	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]
rs10778354	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10778356	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10778357	0.81[EUR][1000 genomes]
rs10861278	0.86[ASN][1000 genomes]
rs10861280	0.87[ASN][1000 genomes]
rs10861282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10861291	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861292	0.81[EUR][1000 genomes]
rs10861293	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10861295	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10861297	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11112208	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs11112221	0.94[ASN][1000 genomes]
rs11112234	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12230637	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs17829927	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2047126	0.85[ASN][1000 genomes]
rs2245695	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2249941	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2252843	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2264883	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2264893	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2453163	0.87[ASN][1000 genomes]
rs2453164	0.87[ASN][1000 genomes]
rs2453169	0.93[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs2463430	0.84[ASN][1000 genomes]
rs2468088	0.83[ASN][1000 genomes]
rs2468094	0.87[ASN][1000 genomes]
rs2468096	0.86[ASN][1000 genomes]
rs2468098	0.86[ASN][1000 genomes]
rs2468103	0.87[ASN][1000 genomes]
rs2468107	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs2468108	0.87[ASN][1000 genomes]
rs2468336	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2468338	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2468339	0.94[CHB][hapmap];0.85[ASN][1000 genomes]
rs2468341	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.87[ASN][1000 genomes]
rs2468342	0.85[ASN][1000 genomes]
rs2468343	0.94[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2468344	0.83[ASN][1000 genomes]
rs2468345	0.83[ASN][1000 genomes]
rs2468396	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2468397	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2642119	0.87[ASN][1000 genomes]
rs2642120	0.94[CHB][hapmap];0.87[ASN][1000 genomes]
rs2730294	0.94[CHB][hapmap];0.81[JPT][hapmap];0.87[ASN][1000 genomes]
rs3890816	0.84[CEU][hapmap]
rs4130161	0.87[CHB][hapmap];0.87[CHD][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs4257060	0.89[CEU][hapmap];0.83[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4537841	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4630370	0.89[CEU][hapmap];0.94[CHB][hapmap];0.87[CHD][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.83[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4644704	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.88[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.91[TSI][hapmap];0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4964116	0.88[CEU][hapmap];0.82[TSI][hapmap]
rs57987047	0.83[EUR][1000 genomes]
rs7961766	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7971260	0.87[ASN][1000 genomes]
rs7971392	0.89[ASN][1000 genomes]
rs7973707	0.81[EUR][1000 genomes]
rs9705471	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[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
rs7959777	GNPTAB	cis	parietal	SCAN
rs7959777	C12orf42	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:105278600-105313800	Weak transcription	Cortex derived primary cultured neurospheres	brain
2	chr12:105284600-105309000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr12:105290800-105331600	Weak transcription	Gastric	stomach
4	chr12:105293400-105310000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr12:105293600-105321600	Weak transcription	A549	lung
6	chr12:105297400-105323600	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:105297600-105323400	Weak transcription	Aorta	Aorta
8	chr12:105297800-105313000	Weak transcription	Fetal Stomach	stomach
9	chr12:105298200-105314600	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr12:105300400-105323200	Weak transcription	Pancreas	Pancrea
11	chr12:105304400-105324600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr12:105304600-105315000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:105304800-105310200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr12:105304800-105313800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr12:105304800-105314800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr12:105305800-105307000	Strong transcription	Liver	Liver
17	chr12:105306600-105307400	Enhancers	Ovary	ovary

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