Variant report

Variant	rs1939747
Chromosome Location	chr11:62911658-62911659
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10736724	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10897369	1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs11231322	1.00[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs11231373	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231374	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs11231375	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11231379	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12364908	1.00[CHB][hapmap];0.86[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[TSI][hapmap]
rs1939743	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1939748	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939749	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939750	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939752	0.90[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939753	0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1939757	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1939758	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1939770	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1939771	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2105623	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2155325	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4121458	0.94[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];1.00[YRI][hapmap]
rs4297470	0.82[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap]
rs4345971	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap]
rs4366490	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4393318	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4405319	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4963246	0.94[ASW][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.86[YRI][hapmap]
rs4963247	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4963248	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6591763	0.81[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6591764	0.81[ASN][1000 genomes]
rs7106537	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs7948969	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap]
rs7952201	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs948060	0.82[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34011	chr11:62652779-62993702	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1045308	chr11:62803635-63109338	Active TSS Weak transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv541059	chr11:62803635-63109338	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv897626	chr11:62839667-62967791	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv555177	chr11:62847518-63110569	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1049725	chr11:62848172-63057827	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv541060	chr11:62848172-63057827	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1047571	chr11:62848172-63109338	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv430397	chr11:62852616-63072310	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv430398	chr11:62881839-62914202	Enhancers Flanking Active TSS Weak transcription	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
11	esv2755674	chr11:62883681-62913852	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv430399	chr11:62883681-62913852	Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
13	esv2753282	chr11:62883681-62986146	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
14	nsv975391	chr11:62910820-62917965	Enhancers Weak transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1939747	TMEM109	cis	parietal	SCAN
rs1939747	BSCL2	cis	cerebellum	SCAN
rs1939747	SNX32	cis	parietal	SCAN
rs1939747	LRFN4	cis	parietal	SCAN

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:62910400-62911800	Weak transcription	HUVEC	blood vessel
2	chr11:62910800-62912600	Enhancers	Fetal Intestine Large	intestine
3	chr11:62911200-62912800	Enhancers	Fetal Intestine Small	intestine
4	chr11:62911400-62914400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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