Variant report

Variant	rs2373857
Chromosome Location	chr2:40609845-40609846
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:68)

rs_ID	r²[population]
rs10165478	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10168748	0.89[CHB][hapmap]
rs10171704	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10177941	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10178405	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10181006	0.89[ASN][1000 genomes]
rs10181007	0.87[AFR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10189274	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10192458	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10192546	0.85[CHB][hapmap]
rs10490051	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.94[JPT][hapmap]
rs11690171	0.85[CHB][hapmap]
rs11691852	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12471797	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12613022	0.83[ASN][1000 genomes]
rs12712692	0.85[CHB][hapmap]
rs12987979	0.85[CHB][hapmap]
rs12988856	0.85[CHB][hapmap]
rs12989200	0.89[CHB][hapmap]
rs12989852	0.85[CHB][hapmap]
rs12995004	0.85[CHB][hapmap]
rs12996962	0.95[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs13012983	1.00[YRI][hapmap]
rs13014950	0.85[CHB][hapmap]
rs13017968	0.95[CHB][hapmap];0.81[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];0.84[ASN][1000 genomes]
rs13022231	1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap]
rs13031340	0.95[CHB][hapmap];0.94[JPT][hapmap];0.85[ASN][1000 genomes]
rs13031441	0.95[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs13032770	0.95[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap]
rs13405065	0.85[CHB][hapmap]
rs1477002	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477004	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1477005	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1558655	0.84[CHB][hapmap]
rs17025840	1.00[ASW][hapmap]
rs1861293	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2192773	0.90[ASN][1000 genomes]
rs2192776	0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2192779	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap];0.97[ASN][1000 genomes]
rs2373859	0.90[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.82[MKK][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2888676	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4446101	0.95[CHB][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4452199	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4452200	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4552227	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4588235	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4645043	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4952409	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6544323	0.85[CHB][hapmap]
rs6544324	0.90[CHB][hapmap]
rs6544330	0.90[CHB][hapmap]
rs6544333	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6544334	0.95[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.88[JPT][hapmap];0.83[MEX][hapmap];0.91[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6718322	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6738580	0.90[CHB][hapmap]
rs6738673	0.85[CHB][hapmap]
rs6745881	0.89[ASN][1000 genomes]
rs6747285	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7424049	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7574340	0.87[ASN][1000 genomes]
rs7598561	0.82[ASN][1000 genomes]
rs7599953	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs918002	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9309055	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs967351	0.83[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs981739	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.88[TSI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs984707	0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[GIH][hapmap];0.88[JPT][hapmap];0.96[MEX][hapmap];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs990270	0.85[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529606	chr2:40206280-40896881	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv873911	chr2:40423454-41161464	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	esv2757794	chr2:40547947-40733776	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv2759044	chr2:40547947-40733776	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv873915	chr2:40573350-40615520	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv1804767	chr2:40601179-40615520	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	esv1805808	chr2:40601179-40615520	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	esv1805510	chr2:40604270-40615520	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1813430	chr2:40604270-40615520	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv873916	chr2:40607504-40649084	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2373857	GALM	cis	parietal	SCAN
rs2373857	EML4	cis	parietal	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:40595000-40611000	Weak transcription	Right Ventricle	heart
2	chr2:40601000-40621800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr2:40607800-40610000	ZNF genes & repeats	Dnd41	blood
4	chr2:40607800-40610600	ZNF genes & repeats	Primary neutrophils fromperipheralblood	blood
5	chr2:40608400-40622000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr2:40608800-40612400	Weak transcription	Colon Smooth Muscle	Colon
7	chr2:40609200-40611000	Weak transcription	Left Ventricle	heart
8	chr2:40609200-40611200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr2:40609200-40612200	Weak transcription	HSMM	muscle
10	chr2:40609400-40611400	Weak transcription	NHDF-Ad	bronchial
11	chr2:40609600-40610400	Weak transcription	Fetal Heart	heart
12	chr2:40609600-40621800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr2:40609800-40610200	Strong transcription	Primary monocytes fromperipheralblood	blood
14	chr2:40609800-40610800	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:40609800-40612200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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