Variant report

Variant	rs4687559
Chromosome Location	chr3:52897842-52897843
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 99 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10865977	0.81[ASN][1000 genomes]
rs11130332	0.85[EUR][1000 genomes]
rs1134546	0.90[EUR][1000 genomes]
rs11707576	0.83[EUR][1000 genomes]
rs11708223	0.85[EUR][1000 genomes]
rs12487379	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12488303	0.81[ASN][1000 genomes]
rs12492391	0.81[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12496077	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12638968	0.85[ASN][1000 genomes]
rs13072536	0.81[ASN][1000 genomes]
rs13072537	0.82[ASN][1000 genomes]
rs13082061	0.86[EUR][1000 genomes]
rs13083728	0.86[ASN][1000 genomes]
rs1573815	0.86[ASN][1000 genomes]
rs2071040	0.81[ASN][1000 genomes]
rs2071041	0.81[ASN][1000 genomes]
rs2072391	0.81[ASN][1000 genomes]
rs2239547	0.80[ASN][1000 genomes]
rs2276815	0.81[ASN][1000 genomes]
rs2276817	0.81[ASN][1000 genomes]
rs2276825	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2336162	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2336664	0.81[ASN][1000 genomes]
rs2336666	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2336667	0.80[ASN][1000 genomes]
rs2336669	0.84[EUR][1000 genomes]
rs2336671	0.81[EUR][1000 genomes]
rs2564947	0.80[EUR][1000 genomes]
rs2581797	0.85[EUR][1000 genomes]
rs2581801	0.85[EUR][1000 genomes]
rs2581802	0.85[EUR][1000 genomes]
rs2581805	0.85[EUR][1000 genomes]
rs2581810	0.89[EUR][1000 genomes]
rs2581815	0.85[EUR][1000 genomes]
rs2581820	0.83[EUR][1000 genomes]
rs2581823	0.82[EUR][1000 genomes]
rs2710342	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2710345	0.85[EUR][1000 genomes]
rs2878762	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35004449	0.80[ASN][1000 genomes]
rs35380116	0.83[EUR][1000 genomes]
rs3733047	0.82[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs3755803	0.81[ASN][1000 genomes]
rs3821873	0.80[ASN][1000 genomes]
rs4302374	1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4350911	0.82[ASN][1000 genomes]
rs4519686	0.84[EUR][1000 genomes]
rs4687554	0.81[ASN][1000 genomes]
rs4687560	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4687562	0.83[ASN][1000 genomes]
rs4687657	0.80[ASN][1000 genomes]
rs4687658	0.81[ASN][1000 genomes]
rs4687663	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4687672	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4687679	0.81[ASN][1000 genomes]
rs4687680	0.87[ASN][1000 genomes]
rs4687682	0.80[ASN][1000 genomes]
rs4687692	0.80[EUR][1000 genomes]
rs56383738	0.81[ASN][1000 genomes]
rs6445538	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445539	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445547	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6445550	0.85[EUR][1000 genomes]
rs6764322	0.82[ASN][1000 genomes]
rs6768844	0.84[EUR][1000 genomes]
rs6770957	0.85[EUR][1000 genomes]
rs6771610	0.83[EUR][1000 genomes]
rs6773040	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6773650	0.82[ASN][1000 genomes]
rs6792578	0.84[EUR][1000 genomes]
rs6795646	0.85[ASN][1000 genomes]
rs6797399	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6798941	0.91[ASN][1000 genomes]
rs7620706	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7621939	0.86[EUR][1000 genomes]
rs7638524	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7648514	0.83[EUR][1000 genomes]
rs7652131	0.85[EUR][1000 genomes]
rs9311485	0.84[EUR][1000 genomes]
rs9682464	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9812543	0.85[EUR][1000 genomes]
rs9813024	0.80[EUR][1000 genomes]
rs9825230	0.81[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9831409	0.85[EUR][1000 genomes]
rs9836178	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9836499	0.81[ASN][1000 genomes]
rs9839035	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9842974	0.84[EUR][1000 genomes]
rs9844736	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9846976	0.84[EUR][1000 genomes]
rs9847024	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9850563	0.80[ASN][1000 genomes]
rs9860296	0.86[ASN][1000 genomes]
rs9865094	0.84[EUR][1000 genomes]
rs9876403	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4687559	ITIH4	Cis_1M	lymphoblastoid	RTeQTL
rs4687559	ITIH4-AS1	cis	Artery Tibial	GTEx
rs4687559	MUSTN1	cis	Artery Aorta	GTEx
rs4687559	ITIH4-AS1	cis	lung	GTEx
rs4687559	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:68 , 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	chr3:52884000-52898200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:52885400-52899600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:52886200-52907800	Weak transcription	NHLF	lung
6	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr3:52886600-52899800	Weak transcription	Dnd41	blood
8	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
9	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
12	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
14	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
17	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
19	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
20	chr3:52887600-52898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
22	chr3:52888000-52898000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
26	chr3:52889200-52898200	Weak transcription	Fetal Muscle Leg	muscle
27	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
29	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
30	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:52891400-52901600	Weak transcription	Right Atrium	heart
32	chr3:52891600-52909400	Weak transcription	Ovary	ovary
33	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
34	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
37	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
38	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
39	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
40	chr3:52894800-52899800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
41	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
42	chr3:52895000-52898600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
44	chr3:52895200-52900400	Weak transcription	Lung	lung
45	chr3:52895400-52899800	Weak transcription	Aorta	Aorta
46	chr3:52895400-52900200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr3:52895400-52904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
48	chr3:52895400-52907400	Weak transcription	Brain Angular Gyrus	brain
49	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr3:52895600-52898200	Weak transcription	Primary neutrophils fromperipheralblood	blood

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