Variant report

Variant	rs4473001
Chromosome Location	chr12:40233146-40233147
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10747886	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10747932	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10784079	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10784118	0.96[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784208	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10784223	0.90[ASN][1000 genomes]
rs10784228	0.92[ASN][1000 genomes]
rs10784234	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10877533	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11173822	0.83[EUR][1000 genomes]
rs12813110	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4293188	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4310675	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4318032	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4350423	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4357761	0.86[ASN][1000 genomes]
rs4370998	0.80[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4382970	0.96[ASN][1000 genomes]
rs4388962	0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4423249	1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4429129	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4433640	0.89[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4473002	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4531537	0.88[CEU][hapmap];0.88[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4539398	0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4579982	0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4598727	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4604958	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4638370	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4638371	1.00[CHB][hapmap];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768188	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4768189	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581365	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6581378	0.82[CEU][hapmap];0.92[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6581403	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6581405	0.92[CHB][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7133478	0.90[YRI][hapmap];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7134335	0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7135701	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7294916	0.85[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7295029	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295344	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7299208	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7304797	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7306234	0.84[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308155	0.89[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7315452	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7358574	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7958983	1.00[CHB][hapmap];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7959259	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7960098	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7961625	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7962260	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963511	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7963645	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7966294	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7967956	0.82[CEU][hapmap];0.93[CHB][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7968509	0.81[CEU][hapmap];0.92[CHB][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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
7	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
8	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 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	chr12:40199200-40265400	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr12:40209200-40268800	Weak transcription	Duodenum Smooth Muscle	Duodenum
4	chr12:40209400-40249800	Weak transcription	Aorta	Aorta
5	chr12:40213000-40248200	Weak transcription	Fetal Intestine Large	intestine
6	chr12:40216000-40246600	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr12:40219800-40272600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr12:40222000-40239600	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr12:40222200-40259400	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr12:40224400-40240400	Weak transcription	Left Ventricle	heart
11	chr12:40224400-40246600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr12:40226400-40275000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
13	chr12:40232600-40233600	Strong transcription	Right Ventricle	heart
14	chr12:40232600-40267800	Weak transcription	Liver	Liver
15	chr12:40232800-40233200	ZNF genes & repeats	Fetal Intestine Small	intestine
16	chr12:40233000-40235200	Strong transcription	Cortex derived primary cultured neurospheres	brain
17	chr12:40233000-40259400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr12:40233000-40259800	Weak transcription	Stomach Smooth Muscle	stomach

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