Variant report

Variant	rs9836499
Chromosome Location	chr3:52904524-52904525
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52903853..52907646-chr3:52911407..52913570,4	K562	blood:
2	chr3:52903586..52906484-chr3:52914418..52917233,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10865977	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11130331	0.91[CEU][hapmap];0.86[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11715347	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11719137	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11915546	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11918800	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11922961	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11922975	0.96[CEU][hapmap];0.86[JPT][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12487379	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12492391	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12629687	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12638968	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13072536	0.90[JPT][hapmap]
rs13072537	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083728	0.95[JPT][hapmap]
rs1573815	0.95[JPT][hapmap]
rs2071042	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2239547	0.95[JPT][hapmap]
rs2240915	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2256332	0.83[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2276815	0.95[JPT][hapmap]
rs2276817	0.95[JPT][hapmap]
rs2276823	0.80[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2276825	0.95[JPT][hapmap]
rs2336558	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2336664	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2336667	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2336668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2535633	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2878762	0.80[ASN][1000 genomes]
rs3733047	0.95[JPT][hapmap]
rs3821873	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4302374	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs4350911	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687554	0.95[JPT][hapmap]
rs4687559	0.81[ASN][1000 genomes]
rs4687560	0.81[ASN][1000 genomes]
rs4687562	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687657	0.95[JPT][hapmap]
rs4687658	0.80[CHB][hapmap];0.95[JPT][hapmap]
rs4687663	0.90[JPT][hapmap]
rs4687672	0.95[JPT][hapmap]
rs4687679	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687680	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687682	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687683	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4687684	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687687	0.96[CEU][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687689	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs56019197	0.83[EUR][1000 genomes]
rs56383738	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60332615	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62253583	0.81[ASN][1000 genomes]
rs6445538	0.95[JPT][hapmap]
rs6445539	0.95[JPT][hapmap]
rs6445541	0.92[CEU][hapmap];0.88[CHB][hapmap];0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs6445547	0.84[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs6764322	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6769789	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6773650	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6795646	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6797399	0.82[ASN][1000 genomes]
rs6803519	0.95[JPT][hapmap]
rs7612624	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7620690	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7626551	0.96[CEU][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7630552	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9682464	0.95[JPT][hapmap]
rs9810807	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9825230	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9839035	0.82[ASN][1000 genomes]
rs9844736	0.80[JPT][hapmap]
rs9850563	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9860296	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9865248	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9866243	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9871175	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9876403	0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs9880619	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9880978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9985365	0.92[CEU][hapmap];0.87[JPT][hapmap];0.84[AMR][1000 genomes];0.96[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs9836499	ITIH4-AS1	cis	lung	GTEx
rs9836499	ITIH4-AS1	cis	Artery Aorta	GTEx
rs9836499	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9836499	ITIH4	cis	Lymphoblastoid	GTEx
rs9836499	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs9836499	FLJ12442	cis	multi-tissue	Pritchard

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52884000-52907400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr3:52886200-52907800	Weak transcription	NHLF	lung
3	chr3:52886600-52907600	Weak transcription	Brain Hippocampus Middle	brain
4	chr3:52886600-52907800	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr3:52886600-52908600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr3:52886600-52911000	Weak transcription	Primary B cells from cord blood	blood
7	chr3:52886600-52920000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr3:52886600-52930200	Weak transcription	Colonic Mucosa	Colon
9	chr3:52886800-52907600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
11	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
12	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
13	chr3:52889800-52909400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr3:52890000-52907800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
15	chr3:52890000-52908600	Weak transcription	Primary T cells fromperipheralblood	blood
16	chr3:52890000-52908800	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:52891600-52909400	Weak transcription	Ovary	ovary
18	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
19	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr3:52892200-52906000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:52892600-52907800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:52894600-52911200	Weak transcription	Stomach Smooth Muscle	stomach
23	chr3:52894800-52907600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr3:52895000-52909000	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr3:52895400-52904600	Weak transcription	Skeletal Muscle Female	skeletal muscle
26	chr3:52895400-52907400	Weak transcription	Brain Angular Gyrus	brain
27	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:52895600-52904800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
30	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
31	chr3:52896200-52909800	Weak transcription	Gastric	stomach
32	chr3:52898400-52907400	Weak transcription	Cortex derived primary cultured neurospheres	brain
33	chr3:52898800-52909600	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr3:52900000-52912800	Weak transcription	Primary B cells from peripheral blood	blood
35	chr3:52900200-52905800	Weak transcription	Dnd41	blood
36	chr3:52900600-52907200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr3:52900600-52909000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr3:52900600-52912200	Weak transcription	Fetal Muscle Leg	muscle
39	chr3:52900800-52907600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr3:52900800-52907600	Weak transcription	Aorta	Aorta
41	chr3:52900800-52909400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
42	chr3:52900800-52912400	Weak transcription	Fetal Muscle Trunk	muscle
43	chr3:52900800-52912800	Weak transcription	Fetal Intestine Small	intestine
44	chr3:52900800-52913000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr3:52901400-52908200	Weak transcription	Monocytes-CD14+_RO01746	blood
46	chr3:52901400-52910200	Weak transcription	Spleen	Spleen
47	chr3:52901800-52912800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr3:52902000-52907600	Weak transcription	Primary monocytes fromperipheralblood	blood
49	chr3:52902000-52907600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr3:52902000-52909400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links