Variant report

Variant	rs2600825
Chromosome Location	chr5:101620464-101620465
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 79 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10434748	0.84[JPT][hapmap]
rs10434749	0.83[JPT][hapmap]
rs10463981	0.84[JPT][hapmap]
rs10515326	0.84[JPT][hapmap]
rs1098806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658397	0.84[JPT][hapmap]
rs1376905	0.89[JPT][hapmap]
rs1376907	0.84[JPT][hapmap]
rs1593077	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17333350	0.84[JPT][hapmap]
rs174414	1.00[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs1982418	0.87[ASW][hapmap];0.84[CEU][hapmap];0.95[GIH][hapmap];0.89[JPT][hapmap];0.92[LWK][hapmap];1.00[MKK][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs2113090	1.00[CHB][hapmap];0.85[JPT][hapmap];0.80[ASN][1000 genomes]
rs2113091	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2113092	0.95[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap];0.88[ASN][1000 genomes]
rs2123136	0.89[JPT][hapmap]
rs2161601	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2263376	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2400800	0.80[AMR][1000 genomes]
rs2548724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600824	0.82[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs2600827	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600828	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2600830	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600832	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600833	0.95[CHB][hapmap];0.90[CHD][hapmap];0.85[JPT][hapmap];0.90[ASN][1000 genomes]
rs2600834	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2600835	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs261098	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261100	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261101	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs261102	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs261103	0.87[ASN][1000 genomes]
rs3096195	0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096196	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3096197	1.00[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs3096213	0.98[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3114659	0.88[GIH][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs3114666	0.88[ASN][1000 genomes]
rs3114667	0.88[ASN][1000 genomes]
rs34688610	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs370176	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs390614	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.95[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs402846	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs416734	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs420900	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs431778	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.83[TSI][hapmap];0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs432190	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs434771	0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs438617	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4386713	0.83[JPT][hapmap]
rs452857	0.89[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62372171	0.84[ASN][1000 genomes]
rs62372211	0.84[ASN][1000 genomes]
rs62372300	0.80[AMR][1000 genomes]
rs6596486	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs6881112	0.84[JPT][hapmap]
rs6884141	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs6893520	0.83[ASN][1000 genomes]
rs709370	0.83[CEU][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs7728630	0.89[JPT][hapmap]
rs7733501	0.83[CEU][hapmap];0.90[JPT][hapmap]
rs7734060	0.88[CEU][hapmap]
rs841752	0.93[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs841920	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs841922	0.84[CEU][hapmap];0.90[JPT][hapmap];0.84[YRI][hapmap];0.84[ASN][1000 genomes]
rs841932	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs841934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs844508	0.90[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs859512	0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022551	chr5:101366177-101649643	Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv882505	chr5:101397849-101652251	Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv1028787	chr5:101432086-101718569	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv817537	chr5:101489151-101992104	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv1016176	chr5:101534391-102333606	Active TSS Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
6	nsv537831	chr5:101534391-102333606	Genic enhancers Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
7	nsv522882	chr5:101596633-101782930	Enhancers Active TSS Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	esv3385694	chr5:101599102-101620704	Flanking Active TSS Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Genic enhancers	n/a	n/a	inside rSNPs	diseases
9	nsv1029894	chr5:101620079-102516827	Enhancers Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2600825	PAM	cis	multi-tissue	Pritchard
rs2600825	PAM	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:101606400-101624400	Weak transcription	Liver	Liver
2	chr5:101613400-101624400	Enhancers	Primary neutrophils fromperipheralblood	blood
3	chr5:101613400-101629400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr5:101614400-101624400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr5:101618000-101623000	Enhancers	Primary hematopoietic stem cells	blood
6	chr5:101618400-101620600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr5:101618600-101620800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
8	chr5:101618600-101624400	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr5:101618800-101620600	Enhancers	Primary B cells from peripheral blood	blood
10	chr5:101619200-101620800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:101619200-101622400	Enhancers	Primary B cells from cord blood	blood
12	chr5:101619200-101630800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
13	chr5:101619600-101624400	Enhancers	Primary hematopoietic stem cells short term culture	blood
14	chr5:101620000-101620600	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr5:101620000-101620600	Enhancers	GM12878-XiMat	blood
16	chr5:101620200-101620800	Enhancers	iPS-15b Cell Line	embryonic stem cell

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