Variant report

Variant	rs10784079
Chromosome Location	chr12:40208037-40208038
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs10747886	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10747932	0.86[CHB][hapmap];0.84[ASN][1000 genomes]
rs10784118	0.90[ASW][hapmap];0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.85[MEX][hapmap];0.82[MKK][hapmap];0.90[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10784208	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784223	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10784228	0.81[ASN][1000 genomes]
rs10784234	0.92[CHB][hapmap];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10877533	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10877733	0.81[JPT][hapmap]
rs10877768	0.81[JPT][hapmap]
rs11173822	0.83[EUR][1000 genomes]
rs11174104	0.91[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap]
rs11174153	0.81[JPT][hapmap]
rs11174238	0.81[JPT][hapmap]
rs11612814	0.81[JPT][hapmap]
rs12813110	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4293188	1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4310675	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4318032	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap]
rs4350423	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4357761	0.94[ASN][1000 genomes]
rs4370998	0.84[ASN][1000 genomes]
rs4382970	0.84[ASN][1000 genomes]
rs4388962	0.86[CHB][hapmap];0.82[CHD][hapmap];0.81[GIH][hapmap];0.84[ASN][1000 genomes]
rs4429129	0.83[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4433640	0.92[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4473001	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4473002	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4531537	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4539398	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4579982	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4598727	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4604958	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4638370	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4638371	0.89[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768188	0.90[ASW][hapmap];0.84[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4768189	0.90[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581365	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6581378	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6581403	0.88[CEU][hapmap];0.81[CHB][hapmap];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6581405	0.83[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7133478	0.86[ASN][1000 genomes]
rs7134335	0.86[ASN][1000 genomes]
rs7135701	1.00[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7294916	1.00[CEU][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7295029	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7295344	0.80[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7298896	0.87[JPT][hapmap]
rs7299208	0.84[CEU][hapmap];0.92[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7304797	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7306234	0.84[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.93[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7308155	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7315452	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7358574	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7958983	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7959259	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7960098	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7961625	0.92[CHB][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7962260	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963511	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7963645	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7966294	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7967956	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7968509	0.96[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs956066	0.81[JPT][hapmap]
rs9668722	0.81[AMR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037457	chr12:39898349-40245401	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv541480	chr12:39898349-40245401	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1052012	chr12:40180398-40237782	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1040628	chr12:40180398-40244001	Strong transcription Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv899025	chr12:40191778-40321846	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv1049214	chr12:40197549-40326495	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40193800-40255800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40194600-40232600	Weak transcription	Right Ventricle	heart
3	chr12:40199200-40265400	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr12:40206200-40221200	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr12:40207600-40210000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr12:40207800-40208200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:40208000-40208200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links