Variant report

Variant	rs7785117
Chromosome Location	chr7:65793761-65793762
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 61 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10261710	0.94[EUR][1000 genomes]
rs1065265	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10950035	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10950036	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10950040	0.89[EUR][1000 genomes]
rs11763224	0.84[EUR][1000 genomes]
rs11766183	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11767262	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11769702	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11770063	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12667200	0.89[ASN][1000 genomes]
rs12668269	0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12670811	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12671152	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12672427	0.91[EUR][1000 genomes]
rs1547529	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17138149	0.92[EUR][1000 genomes]
rs17138156	0.97[EUR][1000 genomes]
rs1862085	0.85[EUR][1000 genomes]
rs1909508	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173571	0.81[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2279757	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2420456	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2420612	0.84[EUR][1000 genomes]
rs35459055	0.89[EUR][1000 genomes]
rs3735147	0.89[EUR][1000 genomes]
rs3936065	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4718325	0.92[EUR][1000 genomes]
rs4718335	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4718346	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4718348	0.81[EUR][1000 genomes]
rs4718364	0.82[EUR][1000 genomes]
rs6460281	0.92[EUR][1000 genomes]
rs6460298	0.89[EUR][1000 genomes]
rs66594357	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs67775320	0.86[EUR][1000 genomes]
rs6945896	0.89[EUR][1000 genomes]
rs6950988	0.85[EUR][1000 genomes]
rs6960848	0.87[EUR][1000 genomes]
rs6961853	0.82[EUR][1000 genomes]
rs6969224	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6970498	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6979636	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73142233	0.92[EUR][1000 genomes]
rs73142245	0.94[EUR][1000 genomes]
rs73142265	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs73146609	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs73148639	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs73148689	0.89[EUR][1000 genomes]
rs73150604	0.90[EUR][1000 genomes]
rs73152714	0.82[EUR][1000 genomes]
rs7782212	0.91[EUR][1000 genomes]
rs7783889	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7786735	0.93[EUR][1000 genomes]
rs7801332	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7810213	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs7811204	0.92[EUR][1000 genomes];0.87[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	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
2	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
3	nsv508458	chr7:65724222-65842639	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
4	nsv1034195	chr7:65743409-65828266	Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7785117	GTF2IRD1P1	cis	Thyroid	GTEx
rs7785117	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs7785117	GS1-124K5.11	cis	Thyroid	GTEx
rs7785117	RNU6-96P	cis	Thyroid	GTEx
rs7785117	GS1-124K5.4	cis	Stomach	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65775600-65795800	Weak transcription	Ovary	ovary
2	chr7:65786600-65797400	Weak transcription	HMEC	breast
3	chr7:65791400-65795800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr7:65791600-65795000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr7:65791800-65797600	Weak transcription	Liver	Liver
6	chr7:65791800-65797800	Weak transcription	HepG2	liver
7	chr7:65791800-65799600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr7:65791800-65800400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr7:65792200-65797200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr7:65792600-65795800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr7:65792600-65795800	Weak transcription	Fetal Stomach	stomach
12	chr7:65792600-65795800	Weak transcription	HSMMtube	muscle
13	chr7:65792600-65796000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr7:65792600-65799800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr7:65792800-65795600	Weak transcription	Osteobl	bone
16	chr7:65792800-65795800	Weak transcription	Fetal Lung	lung
17	chr7:65792800-65795800	Weak transcription	NHLF	lung
18	chr7:65793000-65794000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr7:65793000-65795200	Weak transcription	NHDF-Ad	bronchial
20	chr7:65793000-65795600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr7:65793000-65795600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr7:65793000-65800200	Weak transcription	HSMM	muscle
23	chr7:65793600-65793800	Bivalent Enhancer	ES-UCSF4 Cell Line	embryonic stem cell
24	chr7:65793600-65794000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
25	chr7:65793600-65795200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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