Variant report

Variant	rs12660215
Chromosome Location	chr6:38305770-38305771
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 29 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11758664	1.00[ASN][1000 genomes]
rs12661843	1.00[ASN][1000 genomes]
rs12662422	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12664020	1.00[CHB][hapmap];0.97[GIH][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13193103	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs13197522	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13198868	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13206261	1.00[ASN][1000 genomes]
rs13209118	1.00[ASN][1000 genomes]
rs16890541	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs28360643	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36094313	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60814959	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62397020	1.00[ASN][1000 genomes]
rs6907434	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6917308	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs6938840	1.00[CEU][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs71571312	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs764347	0.91[CEU][hapmap]
rs7762070	1.00[ASN][1000 genomes]
rs7768902	1.00[ASN][1000 genomes]
rs7771835	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs9380755	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1021991	chr6:37893949-38738720	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv885817	chr6:38036420-39019503	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
3	nsv534620	chr6:38049585-38602064	Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv885818	chr6:38147745-38436317	Enhancers Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv885820	chr6:38166511-38468887	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv602957	chr6:38305770-38395874	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12660215	TEAD3	cis	parietal	SCAN
rs12660215	SRSF3	cis	parietal	SCAN

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:38278000-38310600	Weak transcription	Gastric	stomach
2	chr6:38285000-38327800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr6:38291400-38317600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr6:38299200-38313400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
5	chr6:38299800-38317800	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr6:38301600-38305800	Weak transcription	HSMM	muscle
7	chr6:38301600-38306800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr6:38301600-38313400	Weak transcription	Psoas Muscle	Psoas
9	chr6:38301600-38315800	Weak transcription	Brain Hippocampus Middle	brain
10	chr6:38301600-38324600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
11	chr6:38301800-38310400	Weak transcription	Primary B cells from cord blood	blood
12	chr6:38301800-38313400	Weak transcription	Aorta	Aorta
13	chr6:38302000-38310400	Weak transcription	Primary T cells from cord blood	blood
14	chr6:38302000-38315800	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr6:38302000-38318200	Weak transcription	Primary T helper cells PMA-I stimulated	--
16	chr6:38302200-38315800	Weak transcription	Brain Substantia Nigra	brain
17	chr6:38303600-38306800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:38303800-38311000	Weak transcription	Left Ventricle	heart
19	chr6:38304000-38310400	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr6:38304600-38323000	Weak transcription	Ovary	ovary
21	chr6:38304800-38306200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr6:38304800-38306800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr6:38305000-38309400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr6:38305000-38309600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr6:38305000-38317600	Weak transcription	Stomach Smooth Muscle	stomach
26	chr6:38305000-38318000	Weak transcription	Colon Smooth Muscle	Colon
27	chr6:38305400-38305800	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr6:38305400-38306400	Enhancers	NHDF-Ad	bronchial
29	chr6:38305400-38306600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr6:38305600-38305800	Enhancers	Pancreas	Pancrea
31	chr6:38305600-38306000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr6:38305600-38306000	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr6:38305600-38306200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
34	chr6:38305600-38306400	Enhancers	HSMMtube	muscle
35	chr6:38305600-38306400	Enhancers	NHEK	skin
36	chr6:38305600-38306400	Enhancers	Osteobl	bone
37	chr6:38305600-38306800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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