Variant report

Variant	rs12487379
Chromosome Location	chr3:52895785-52895786
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52883267..52885377-chr3:52893903..52896581,2	K562	blood:

Extended variants
information (count: 62 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10865977	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130331	0.88[EUR][1000 genomes]
rs11715347	0.91[EUR][1000 genomes]
rs11719137	0.90[EUR][1000 genomes]
rs11915546	0.90[EUR][1000 genomes]
rs11918800	0.89[EUR][1000 genomes]
rs11922961	0.89[EUR][1000 genomes]
rs11922975	0.85[EUR][1000 genomes]
rs12492391	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12629687	0.87[EUR][1000 genomes]
rs12638968	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13072537	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2276823	0.87[EUR][1000 genomes]
rs2336558	0.91[EUR][1000 genomes]
rs2336664	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336666	0.83[ASN][1000 genomes]
rs2336667	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2336668	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2878762	0.88[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs3821873	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4302374	0.86[ASN][1000 genomes]
rs4350911	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687559	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4687560	0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs4687562	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687679	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687680	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687682	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687683	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687684	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4687687	0.88[EUR][1000 genomes]
rs4687689	0.88[EUR][1000 genomes]
rs56019197	0.90[EUR][1000 genomes]
rs56383738	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60332615	0.90[EUR][1000 genomes]
rs6445541	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6445547	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs6764322	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6769789	0.91[EUR][1000 genomes]
rs6773650	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6795646	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6797399	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs7612624	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7620690	0.93[EUR][1000 genomes]
rs7626551	0.85[EUR][1000 genomes]
rs7630552	0.93[EUR][1000 genomes]
rs9810807	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9825230	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9836499	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839035	0.84[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs9850563	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9860296	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9865248	0.83[EUR][1000 genomes]
rs9866243	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9871175	0.88[EUR][1000 genomes]
rs9876403	0.84[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs9880619	0.88[EUR][1000 genomes]
rs9880978	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9985365	0.81[AMR][1000 genomes];0.88[EUR][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12487379	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs12487379	ITIH4-AS1	cis	lung	GTEx
rs12487379	ITIH4-AS1	cis	Artery Tibial	GTEx
rs12487379	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:76 , 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	chr3:52886600-52897600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr3:52886600-52897600	Weak transcription	Fetal Intestine Small	intestine
8	chr3:52886600-52897800	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr3:52886600-52898200	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr3:52886600-52899800	Weak transcription	Dnd41	blood
11	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
12	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
15	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
17	chr3:52886800-52900400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr3:52887000-52898000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr3:52887000-52898600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
22	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr3:52887600-52898000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
25	chr3:52888000-52898000	Weak transcription	Primary B cells from peripheral blood	blood
26	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
27	chr3:52888000-52900000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:52888600-52902600	Weak transcription	Brain Anterior Caudate	brain
29	chr3:52889000-52897800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr3:52889200-52898200	Weak transcription	Fetal Muscle Leg	muscle
31	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr3:52890000-52896800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr3:52891400-52901600	Weak transcription	Right Atrium	heart
37	chr3:52891600-52909400	Weak transcription	Ovary	ovary
38	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
39	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
40	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr3:52892600-52903200	Weak transcription	Brain Substantia Nigra	brain
42	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr3:52894200-52895800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:52894200-52896000	Strong transcription	Thymus	Thymus
45	chr3:52894200-52896400	Strong transcription	Fetal Stomach	stomach
46	chr3:52894400-52895800	Strong transcription	Liver	Liver
47	chr3:52894400-52896000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
48	chr3:52894600-52904000	Weak transcription	Pancreas	Pancrea
49	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:52894800-52896200	Strong transcription	Gastric	stomach

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