Variant report

Variant	rs761136
Chromosome Location	chr6:53823767-53823768
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs12196155	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1543356	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2223617	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2473599	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2473601	0.85[EUR][1000 genomes]
rs2494087	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2494089	0.85[EUR][1000 genomes]
rs2494090	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2494091	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2745460	0.87[EUR][1000 genomes]
rs2820217	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs2820218	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2894816	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4077760	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs4276504	1.00[CHB][hapmap]
rs4357137	1.00[JPT][hapmap]
rs4476827	0.82[CHB][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.81[TSI][hapmap]
rs6903532	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6905927	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs761135	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs763814	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7752800	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7772783	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382261	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382262	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382264	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9464005	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9474672	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]

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	nsv1034955	chr6:53447607-53931055	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830664	chr6:53698021-53825270	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
3	nsv1067663	chr6:53796341-54449718	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv529158	chr6:53796341-54449718	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs761136	FBXO9	cis	parietal	SCAN
rs761136	LRRC1	cis	parietal	SCAN
rs761136	COL21A1	cis	cerebellum	SCAN
rs761136	C6orf142	cis	cerebellum	SCAN
rs761136	TFAP2D	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:53795600-53826200	Weak transcription	NHEK	skin
2	chr6:53811400-53825000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr6:53819000-53827000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:53821400-53824200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr6:53821400-53824200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:53821400-53824400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr6:53821600-53826400	Weak transcription	HUES6 Cell Line	embryonic stem cell

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