Variant report

Variant	rs60332615
Chromosome Location	chr3:52867595-52867596
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 46 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10865977	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715347	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11719137	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11915546	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11918800	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11922961	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12487379	0.90[EUR][1000 genomes]
rs12638968	0.81[EUR][1000 genomes]
rs13072537	0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2239548	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240915	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2240917	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245538	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2245647	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2256332	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2276823	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2336558	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2336664	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2336667	0.82[EUR][1000 genomes]
rs2336668	0.82[EUR][1000 genomes]
rs2535633	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3774364	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4350911	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4687562	0.80[EUR][1000 genomes]
rs4687679	0.81[EUR][1000 genomes]
rs4687682	0.82[AMR][1000 genomes]
rs4687683	0.82[EUR][1000 genomes]
rs56019197	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56383738	0.81[ASN][1000 genomes]
rs6445541	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6764322	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6769789	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6773650	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7612624	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7617468	0.86[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs7620690	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7630552	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7652667	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9836499	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9850563	0.81[AMR][1000 genomes]

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	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
4	esv1810629	chr3:52817031-52869635	Weak transcription Active TSS Strong transcription Bivalent Enhancer Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv876797	chr3:52817675-52873984	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv3435205	chr3:52867536-52867892	Weak transcription Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Enhancers Active TSS	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs60332615	ITIH4-AS1	cis	lung	GTEx
rs60332615	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs60332615	ITIH4-AS1	cis	Artery Tibial	GTEx
rs60332615	ITIH4-AS1	cis	Artery Aorta	GTEx
rs60332615	ITIH4-AS1	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
2	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
3	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
4	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
9	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
10	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
11	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr3:52858800-52868800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr3:52858800-52868800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr3:52858800-52869200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr3:52859400-52869000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr3:52860200-52869000	Weak transcription	Fetal Intestine Small	intestine
19	chr3:52861200-52868800	Weak transcription	Lung	lung
20	chr3:52862000-52869200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
21	chr3:52862000-52882600	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr3:52863200-52872600	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr3:52864400-52875800	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr3:52865000-52867800	Enhancers	Psoas Muscle	Psoas
25	chr3:52865000-52869400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr3:52865200-52869000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr3:52865600-52867600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr3:52865600-52874200	Weak transcription	Sigmoid Colon	Sigmoid Colon
29	chr3:52865600-52875200	Weak transcription	Dnd41	blood
30	chr3:52865800-52869000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr3:52865800-52878600	Weak transcription	Small Intestine	intestine
32	chr3:52866000-52868200	Weak transcription	Brain Angular Gyrus	brain
33	chr3:52866000-52868400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr3:52866000-52869800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr3:52866000-52884800	Weak transcription	HMEC	breast
36	chr3:52866200-52867600	Weak transcription	Right Atrium	heart
37	chr3:52866200-52867800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr3:52866200-52868200	Weak transcription	Ovary	ovary
39	chr3:52866200-52868400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:52866200-52868600	Transcr. at gene 5' and 3'	Skeletal Muscle Male	skeletal muscle
41	chr3:52866200-52869000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:52866200-52869200	Weak transcription	Placenta	Placenta
43	chr3:52866200-52869600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
44	chr3:52866200-52870200	Weak transcription	Gastric	stomach
45	chr3:52866200-52872600	Weak transcription	Duodenum Mucosa	Duodenum
46	chr3:52866200-52872600	Weak transcription	Esophagus	oesophagus
47	chr3:52866200-52885200	Weak transcription	NHEK	skin
48	chr3:52866400-52867600	Strong transcription	Brain Anterior Caudate	brain
49	chr3:52866400-52867800	Weak transcription	Left Ventricle	heart
50	chr3:52866400-52867800	Weak transcription	Right Ventricle	heart

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