Variant report

Variant	rs4682410
Chromosome Location	chr3:112201930-112201931
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs12632867	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.87[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1386895	0.83[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398091	0.82[CEU][hapmap];0.81[GIH][hapmap];0.80[EUR][1000 genomes]
rs1512006	0.94[ASW][hapmap];0.88[CHB][hapmap];0.92[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs1814052	0.90[EUR][1000 genomes]
rs1844089	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs1873571	0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs1877363	0.94[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs2171513	0.91[TSI][hapmap]
rs2171514	0.87[EUR][1000 genomes]
rs2633555	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2633556	0.87[EUR][1000 genomes]
rs2633557	0.97[EUR][1000 genomes]
rs2633560	0.97[EUR][1000 genomes]
rs2633562	0.82[CEU][hapmap];0.91[GIH][hapmap];0.91[TSI][hapmap];0.97[EUR][1000 genomes]
rs2633563	0.93[EUR][1000 genomes]
rs2633578	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2633579	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs2633580	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2633582	0.94[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2633584	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2633588	0.90[EUR][1000 genomes]
rs2633589	0.90[EUR][1000 genomes]
rs2638013	0.90[EUR][1000 genomes]
rs2638015	0.87[EUR][1000 genomes]
rs2638016	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2638017	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2638022	0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2638031	0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2638037	0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs2638039	0.83[CHB][hapmap]
rs2705517	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2705525	0.90[EUR][1000 genomes]
rs2705531	0.84[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs2705532	0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2705533	0.90[EUR][1000 genomes]
rs2705534	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs2705536	0.90[EUR][1000 genomes]
rs2705544	0.82[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs2705555	0.97[EUR][1000 genomes]
rs2705559	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2705565	0.82[CEU][hapmap];0.91[GIH][hapmap];0.90[EUR][1000 genomes]
rs2705566	0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2952323	0.94[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2952326	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2952327	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2971204	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs4519670	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4682413	0.82[AMR][1000 genomes]
rs6438079	0.94[ASW][hapmap];0.82[CEU][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6774355	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs6792947	0.94[ASW][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs7652377	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs766968	0.94[ASW][hapmap];0.88[CHB][hapmap];0.95[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.90[YRI][hapmap]
rs9288952	0.82[CHB][hapmap];0.87[CHD][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes]
rs9756562	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9848054	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9854043	0.84[AMR][1000 genomes]
rs9866734	0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap]
rs9869455	0.93[JPT][hapmap];0.90[YRI][hapmap]
rs9869579	0.82[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.90[YRI][hapmap]
rs998036	0.82[CHB][hapmap]

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	nsv591294	chr3:112091220-112208750	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv1010208	chr3:112098542-112227212	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1003936	chr3:112125931-112274613	Weak transcription Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv998309	chr3:112130290-112278804	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv591300	chr3:112144026-112270857	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
6	nsv1006065	chr3:112147080-112276983	Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1005323	chr3:112171990-112274613	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv877342	chr3:112185025-112332629	Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4682410	SLC35A5	cis	lymphoblastoid	seeQTL

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:112194200-112214000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr3:112197000-112203800	Genic enhancers	Primary B cells from peripheral blood	blood
3	chr3:112197400-112202200	Genic enhancers	Primary B cells from cord blood	blood
4	chr3:112199200-112203600	Enhancers	Primary T helper cells fromperipheralblood	blood
5	chr3:112199800-112202600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:112199800-112202600	Enhancers	Primary T killer memory cells from peripheral blood	blood
7	chr3:112200000-112202400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr3:112200200-112202400	Enhancers	Primary T cells from cord blood	blood
9	chr3:112200200-112203800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
10	chr3:112200400-112214800	Weak transcription	Fetal Thymus	thymus
11	chr3:112200600-112203400	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr3:112200600-112208600	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:112200600-112217000	Weak transcription	Sigmoid Colon	Sigmoid Colon
14	chr3:112201200-112202200	Flanking Active TSS	GM12878-XiMat	blood
15	chr3:112201400-112208600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:112201400-112215600	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:112201600-112202600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
18	chr3:112201800-112202200	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr3:112201800-112202600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr3:112201800-112203600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
21	chr3:112201800-112208600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links