Variant report

Variant	rs17409637
Chromosome Location	chr4:87247384-87247385
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1031739	0.92[CEU][hapmap];0.89[CHB][hapmap];0.81[JPT][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes]
rs1460752	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17408832	1.00[CEU][hapmap];0.88[CHB][hapmap];0.83[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs17409478	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17417758	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17449147	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes]
rs17449582	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17451111	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869423	1.00[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2869433	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2869434	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35103650	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4299551	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4521313	0.83[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4693140	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693762	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4693763	1.00[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.86[LWK][hapmap];0.92[TSI][hapmap];0.88[AMR][1000 genomes]
rs4693769	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55681806	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs55724430	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56255533	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57869802	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58538747	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs60753208	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62305543	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62305546	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62307365	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62307366	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs62307367	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62307409	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs62307454	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62308361	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62308365	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6827483	1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[JPT][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs72663972	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7376405	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7688651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

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	nsv1003585	chr4:86957967-87250436	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv594786	chr4:87076360-87609320	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	7 gene(s)	inside rSNPs	diseases
3	nsv999470	chr4:87165663-87514552	Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
4	nsv537164	chr4:87165663-87514552	Enhancers Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	6 gene(s)	inside rSNPs	diseases
5	nsv934210	chr4:87197339-87325578	Weak transcription Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1011494	chr4:87221480-87257453	Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
7	nsv594787	chr4:87221827-87888667	Enhancers Weak transcription Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
8	nsv1007891	chr4:87230601-87252524	Strong transcription Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv461574	chr4:87239764-87279096	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv594788	chr4:87239764-87279096	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17409637	SLC6A4	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87232600-87247400	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr4:87235200-87250200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr4:87239400-87252400	Weak transcription	Brain Angular Gyrus	brain
4	chr4:87239400-87254400	Weak transcription	Brain Hippocampus Middle	brain
5	chr4:87239400-87258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr4:87242000-87270000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr4:87243800-87247600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr4:87247000-87248000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr4:87247200-87247600	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr4:87247200-87247600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr4:87247200-87247800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr4:87247200-87247800	Enhancers	Primary hematopoietic stem cells short term culture	blood
13	chr4:87247200-87247800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr4:87247200-87248200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr4:87247200-87248200	Enhancers	Muscle Satellite Cultured Cells	--

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links