Variant report

Variant	rs12638968
Chromosome Location	chr3:52919447-52919448
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

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

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

rs_ID	r²[population]
rs10865977	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130331	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11715347	0.83[EUR][1000 genomes]
rs11719137	0.81[EUR][1000 genomes]
rs11915546	0.82[EUR][1000 genomes]
rs11918800	0.81[EUR][1000 genomes]
rs11922961	0.81[EUR][1000 genomes]
rs11922975	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12487379	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492391	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629687	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs13072537	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2336558	0.83[EUR][1000 genomes]
rs2336664	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336666	0.86[ASN][1000 genomes]
rs2336667	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2336668	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2878762	0.88[ASN][1000 genomes]
rs3821873	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4302374	0.86[ASN][1000 genomes]
rs4350911	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4687559	0.85[ASN][1000 genomes]
rs4687560	0.85[ASN][1000 genomes]
rs4687562	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687679	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687680	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687682	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687683	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687684	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687687	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4687689	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs56019197	0.82[EUR][1000 genomes]
rs56383738	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs60332615	0.81[EUR][1000 genomes]
rs62253583	0.80[EUR][1000 genomes]
rs6445541	0.82[EUR][1000 genomes]
rs6445547	0.86[ASN][1000 genomes]
rs6764322	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6769789	0.82[EUR][1000 genomes]
rs6773650	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6795646	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797399	0.86[ASN][1000 genomes]
rs7612624	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7620690	0.84[EUR][1000 genomes]
rs7626551	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7630552	0.84[EUR][1000 genomes]
rs9810807	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9825230	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9836499	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9839035	0.86[ASN][1000 genomes]
rs9850563	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9860296	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9865248	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9866243	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9871175	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9876403	0.87[ASN][1000 genomes]
rs9880619	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9880978	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9985365	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12638968	ITIH4-AS1	cis	lung	GTEx
rs12638968	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs12638968	ITIH4-AS1	cis	Artery Tibial	GTEx
rs12638968	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
3	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
5	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
6	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
8	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
9	chr3:52902200-52925200	Weak transcription	Placenta	Placenta
10	chr3:52905000-52919800	Weak transcription	Right Ventricle	heart
11	chr3:52906000-52924400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:52908000-52924000	Weak transcription	Brain Hippocampus Middle	brain
13	chr3:52908000-52924000	Weak transcription	Brain Substantia Nigra	brain
14	chr3:52908200-52919600	Weak transcription	HSMM	muscle
15	chr3:52908200-52925400	Weak transcription	Brain Anterior Caudate	brain
16	chr3:52908200-52925400	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr3:52908400-52924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr3:52908400-52924600	Weak transcription	NHLF	lung
19	chr3:52908400-52930600	Weak transcription	A549	lung
20	chr3:52908600-52924600	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr3:52909200-52920000	Weak transcription	Liver	Liver
23	chr3:52909200-52925200	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr3:52909600-52925400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr3:52909800-52925200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr3:52909800-52925400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
27	chr3:52910000-52929400	Weak transcription	HMEC	breast
28	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr3:52910200-52920200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr3:52910200-52925400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
31	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
34	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
35	chr3:52910400-52920200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
36	chr3:52910400-52924800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
37	chr3:52910400-52930200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr3:52910600-52926400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr3:52911600-52921400	Weak transcription	Spleen	Spleen
40	chr3:52912400-52919600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr3:52913000-52919600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr3:52913200-52919800	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:52913200-52926600	Weak transcription	K562	blood
44	chr3:52913400-52919600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr3:52913400-52920200	Weak transcription	Pancreas	Pancrea
46	chr3:52913600-52924600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
47	chr3:52913600-52925200	Weak transcription	Adipose Nuclei	Adipose
48	chr3:52913800-52919600	Weak transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:52913800-52924200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr3:52914000-52921400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain

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