Variant report

Variant	rs4713858
Chromosome Location	chr6:35402785-35402786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 40 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1040436	0.88[CHD][hapmap]
rs1053049	0.88[CHD][hapmap]
rs1883322	0.86[CHD][hapmap]
rs2016520	0.90[CHD][hapmap]
rs2038067	0.81[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs2038068	0.86[CHD][hapmap]
rs2076166	0.88[CEU][hapmap];0.92[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2076167	0.88[CHD][hapmap]
rs2076169	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs2267665	0.83[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs2267666	0.86[CHD][hapmap]
rs2267667	0.86[CHD][hapmap]
rs2267668	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2267669	0.83[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs2894401	0.85[CHB][hapmap];0.85[CHD][hapmap];0.94[LWK][hapmap]
rs3734254	0.90[CHD][hapmap]
rs6457818	0.81[EUR][1000 genomes]
rs6457819	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6899536	0.84[ASN][1000 genomes]
rs760783	0.81[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7749160	0.88[CEU][hapmap];0.92[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7751481	0.86[CHD][hapmap]
rs9380506	0.81[ASN][1000 genomes]
rs9462082	0.94[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9462083	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9462084	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9470015	0.94[CEU][hapmap];0.86[CHB][hapmap];0.83[JPT][hapmap];0.82[ASN][1000 genomes]
rs9470024	0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9794	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv462907	chr6:35333799-35408959	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv602908	chr6:35333799-35408959	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv602909	chr6:35356640-35423489	Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv470812	chr6:35374461-35418118	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
6	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
7	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
8	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
9	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
10	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
11	nsv885800	chr6:35394247-35406153	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Height	18391951	GWAS catalog

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4713858	C6orf106	cis	cerebellum	SCAN
rs4713858	RPL10A	cis	parietal	SCAN
rs4713858	KIF6	cis	parietal	SCAN
rs4713858	C6orf81	cis	parietal	SCAN
rs4713858	DEF6	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35392600-35402800	Weak transcription	Colon Smooth Muscle	Colon
2	chr6:35394600-35403000	Weak transcription	Brain Germinal Matrix	brain
3	chr6:35395200-35404400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr6:35395600-35402800	Weak transcription	Psoas Muscle	Psoas
5	chr6:35395800-35403000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr6:35395800-35403200	Weak transcription	Fetal Muscle Trunk	muscle
7	chr6:35397200-35403400	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr6:35397400-35403000	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:35397400-35403600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
10	chr6:35397600-35403200	Weak transcription	Brain Hippocampus Middle	brain
11	chr6:35398200-35402800	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:35398400-35404400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr6:35400200-35402800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr6:35400200-35403400	Weak transcription	Small Intestine	intestine
15	chr6:35400400-35402800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr6:35400400-35402800	Weak transcription	Liver	Liver
17	chr6:35400400-35402800	Weak transcription	Fetal Intestine Large	intestine
18	chr6:35400400-35403000	Weak transcription	Spleen	Spleen
19	chr6:35400600-35413800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr6:35401800-35405000	Enhancers	Duodenum Mucosa	Duodenum
21	chr6:35402000-35405800	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr6:35402200-35403600	Enhancers	Left Ventricle	heart
23	chr6:35402200-35403600	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr6:35402200-35403800	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr6:35402200-35404200	Enhancers	Adipose Nuclei	Adipose
26	chr6:35402400-35402800	Enhancers	Rectal Mucosa Donor 29	rectum
27	chr6:35402400-35402800	Weak transcription	Right Ventricle	heart
28	chr6:35402400-35403000	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr6:35402600-35403000	Weak transcription	Colonic Mucosa	Colon
30	chr6:35402600-35403800	Enhancers	Fetal Heart	heart

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