Variant report

Variant	rs7620706
Chromosome Location	chr3:52891756-52891757
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs12488303	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs12496077	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072536	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs13083728	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1573815	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2001735	0.85[ASN][1000 genomes]
rs2071040	0.91[ASN][1000 genomes]
rs2071041	0.91[ASN][1000 genomes]
rs2072391	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2239547	0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2276815	0.82[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2276817	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2276825	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2336666	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2878762	0.86[ASN][1000 genomes]
rs35004449	0.90[ASN][1000 genomes]
rs3733047	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3755803	0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4302374	0.85[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs4687554	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4687559	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687560	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4687657	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4687658	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4687663	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4687672	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445538	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445539	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445541	0.81[ASN][1000 genomes]
rs6445547	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6797399	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6798941	0.95[ASN][1000 genomes]
rs7638524	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9682464	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9839035	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs9876403	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834698	chr3:52749983-52928219	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	27 gene(s)	inside rSNPs	diseases
2	esv2762328	chr3:52774884-53002150	Strong transcription Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	esv3446915	chr3:52786850-53049217	Strong transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs7620706	ITIH4-AS1	cis	lung	GTEx
rs7620706	MUSTN1	cis	Artery Aorta	GTEx
rs7620706	ITIH4-AS1	cis	Artery Aorta	GTEx
rs7620706	MUSTN1	cis	Thyroid	GTEx
rs7620706	ITIH4-AS1	cis	Artery Tibial	GTEx
rs7620706	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs7620706	TMEM110	cis	Muscle Skeletal	GTEx
rs7620706	ITIH4-AS1	cis	Whole Blood	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52870000-52901000	Weak transcription	Fetal Brain Male	brain
2	chr3:52873400-52892000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr3:52879800-52894800	Weak transcription	HSMM	muscle
4	chr3:52883400-52894200	Weak transcription	HSMMtube	muscle
5	chr3:52883400-52894600	Weak transcription	Hela-S3	cervix
6	chr3:52883800-52894400	Weak transcription	Psoas Muscle	Psoas
7	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr3:52884200-52893000	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr3:52884400-52893000	Weak transcription	Small Intestine	intestine
11	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:52886200-52907800	Weak transcription	NHLF	lung
13	chr3:52886400-52894200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
14	chr3:52886600-52894400	Weak transcription	Esophagus	oesophagus
15	chr3:52886600-52894400	Weak transcription	Gastric	stomach
16	chr3:52886600-52894600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr3:52886600-52894600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr3:52886600-52895000	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
21	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr3:52886600-52899800	Weak transcription	Dnd41	blood
24	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
25	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
26	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
27	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
28	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
30	chr3:52886800-52891800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:52886800-52893600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr3:52886800-52894400	Weak transcription	Placenta	Placenta
33	chr3:52886800-52894600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr3:52886800-52894800	Weak transcription	Brain Angular Gyrus	brain
35	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
40	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr3:52887400-52891800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr3:52887400-52894400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr3:52887600-52894200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr3:52887600-52894200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr3:52887600-52894600	Weak transcription	Fetal Muscle Trunk	muscle
46	chr3:52887600-52898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
48	chr3:52888000-52894400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
49	chr3:52888000-52898000	Weak transcription	Primary B cells from peripheral blood	blood
50	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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