Variant report

Variant	rs4693140
Chromosome Location	chr4:87240799-87240800
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1031739	1.00[CEU][hapmap];0.83[CHB][hapmap];0.89[CHD][hapmap];0.81[GIH][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1460752	0.84[AMR][1000 genomes]
rs17408832	0.92[CEU][hapmap];0.82[CHB][hapmap];0.83[AMR][1000 genomes]
rs17409478	0.91[CEU][hapmap];0.94[CHB][hapmap];0.83[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17409637	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]
rs17417758	0.92[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17449147	0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes]
rs17449582	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17451111	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869423	0.92[CEU][hapmap];0.81[CHB][hapmap];0.87[AMR][1000 genomes]
rs2869433	0.92[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.80[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2869434	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35103650	0.83[AMR][1000 genomes]
rs4299551	0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs4521313	0.94[CHB][hapmap];0.80[JPT][hapmap];0.87[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs4693762	0.84[AMR][1000 genomes]
rs4693763	0.92[CEU][hapmap];0.83[CHB][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap];0.87[AMR][1000 genomes]
rs4693769	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs55681806	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs55724430	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs56255533	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs57869802	0.87[AMR][1000 genomes]
rs58538747	0.84[AMR][1000 genomes]
rs60753208	0.87[AMR][1000 genomes]
rs62305543	0.85[AMR][1000 genomes]
rs62305546	0.84[AMR][1000 genomes]
rs62307365	0.87[AMR][1000 genomes]
rs62307366	0.87[AMR][1000 genomes]
rs62307367	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62307409	0.82[ASN][1000 genomes]
rs62307454	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62308361	0.87[AMR][1000 genomes]
rs62308365	0.83[AMR][1000 genomes]
rs6827483	0.95[CEU][hapmap];0.81[CHB][hapmap];0.84[AMR][1000 genomes]
rs72663972	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7376405	0.83[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs7688651	0.92[CEU][hapmap];0.94[CHB][hapmap];0.84[JPT][hapmap];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4693140	SLC6A4	trans	lymphoblastoid	seeQTL
rs4693140	MAPK10	cis	lesional skin	skin_eQTL

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:87224000-87242600	Weak transcription	Fetal Stomach	stomach
2	chr4:87232600-87247400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr4:87235200-87250200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
4	chr4:87235800-87242200	Weak transcription	Fetal Brain Male	brain
5	chr4:87239200-87240800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr4:87239400-87252400	Weak transcription	Brain Angular Gyrus	brain
7	chr4:87239400-87254400	Weak transcription	Brain Hippocampus Middle	brain
8	chr4:87239400-87258600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr4:87240000-87241800	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr4:87240200-87241200	Enhancers	HMEC	breast
11	chr4:87240600-87241000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr4:87240600-87241200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr4:87240600-87241200	Enhancers	NHEK	skin

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