Variant report

Variant	rs17387199
Chromosome Location	chr4:86440758-86440759
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10017712	0.82[CHD][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.83[MEX][hapmap];0.84[ASN][1000 genomes]
rs10020489	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10029852	1.00[CHB][hapmap];0.93[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.87[MEX][hapmap];0.86[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs10032314	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1031988	0.83[MEX][hapmap]
rs11946933	0.82[ASN][1000 genomes]
rs12500479	0.90[ASN][1000 genomes]
rs12501745	1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[ASN][1000 genomes]
rs12506009	0.83[MEX][hapmap]
rs12506039	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12506596	0.83[MEX][hapmap]
rs12510597	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[JPT][hapmap];0.91[ASN][1000 genomes]
rs12510645	0.91[ASN][1000 genomes]
rs12640411	0.83[MEX][hapmap]
rs12644974	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13139321	0.91[ASN][1000 genomes]
rs13140816	0.91[ASN][1000 genomes]
rs1384135	0.83[MEX][hapmap]
rs1545823	0.87[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17387344	0.87[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17389300	0.83[MEX][hapmap]
rs1871824	0.89[ASN][1000 genomes]
rs1871825	0.89[ASN][1000 genomes]
rs1994065	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1994068	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2062080	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2869352	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2869355	0.82[ASN][1000 genomes]
rs4693703	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4693704	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4693716	0.83[MEX][hapmap]
rs6838692	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6839494	0.93[ASN][1000 genomes]
rs7657835	0.93[ASN][1000 genomes]
rs964837	1.00[CHB][hapmap]
rs9994597	0.82[ASN][1000 genomes]
rs9994823	0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv461566	chr4:85988032-86725502	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
3	nsv594747	chr4:85988032-86725502	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
4	nsv470048	chr4:85998783-86720838	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs17387199	TIGD2	cis	cerebellum	SCAN
rs17387199	ARHGAP24	cis	lymphoblastoid	seeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86419800-86442200	Weak transcription	Left Ventricle	heart
2	chr4:86430200-86443200	Weak transcription	Spleen	Spleen
3	chr4:86430200-86468600	Weak transcription	Pancreas	Pancrea
4	chr4:86431800-86443600	Weak transcription	Fetal Lung	lung
5	chr4:86434600-86444000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr4:86435400-86449200	Weak transcription	Primary B cells from cord blood	blood
7	chr4:86435600-86442800	Weak transcription	Monocytes-CD14+_RO01746	blood
8	chr4:86436200-86444000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:86436400-86442000	Weak transcription	HSMMtube	muscle
10	chr4:86436400-86442400	Weak transcription	HSMM	muscle
11	chr4:86436400-86455600	Weak transcription	Gastric	stomach
12	chr4:86437400-86441800	Weak transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:86439200-86442200	Weak transcription	Fetal Heart	heart
14	chr4:86440000-86443000	Genic enhancers	Primary B cells from peripheral blood	blood

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