Variant report

Variant	rs9860296
Chromosome Location	chr3:52913781-52913782
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52908141..52910474-chr3:52911838..52914428,2	K562	blood:

Extended variants
information (count: 83 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:80)

rs_ID	r²[population]
rs10865977	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11130331	0.92[CEU][hapmap];0.85[CHD][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11715347	0.80[EUR][1000 genomes]
rs11918800	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.89[TSI][hapmap]
rs11922961	0.96[CEU][hapmap];0.86[CHB][hapmap];0.82[CHD][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs11922975	0.96[CEU][hapmap];0.87[CHD][hapmap];0.86[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12487379	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12492391	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629687	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12638968	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13072536	0.90[JPT][hapmap]
rs13072537	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13083728	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs1573815	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2071042	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap]
rs2239547	0.82[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2240915	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs2256332	0.83[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.80[MEX][hapmap];0.82[TSI][hapmap]
rs2257216	0.82[YRI][hapmap]
rs2276815	0.95[JPT][hapmap]
rs2276817	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2276825	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs2336558	0.80[EUR][1000 genomes]
rs2336664	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2336666	0.86[ASN][1000 genomes]
rs2336667	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2336668	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2336670	0.82[YRI][hapmap]
rs2535633	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.85[MEX][hapmap];0.87[TSI][hapmap]
rs2878762	0.87[ASN][1000 genomes]
rs3617	0.80[MEX][hapmap]
rs3733047	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs3821873	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4302374	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs4350911	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687554	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs4687559	0.86[ASN][1000 genomes]
rs4687560	0.86[ASN][1000 genomes]
rs4687562	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4687657	0.82[CHD][hapmap];0.95[JPT][hapmap]
rs4687658	0.83[CHB][hapmap];0.95[JPT][hapmap]
rs4687663	0.90[JPT][hapmap]
rs4687672	0.95[JPT][hapmap]
rs4687679	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4687680	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687682	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4687683	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4687684	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4687687	0.96[CEU][hapmap];0.87[CHD][hapmap];0.91[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4687689	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56383738	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6445538	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs6445539	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs6445541	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs6445547	0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs6764322	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6769789	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap]
rs6773650	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6795646	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6797399	0.86[ASN][1000 genomes]
rs6803519	0.84[CHD][hapmap];0.95[JPT][hapmap]
rs7612624	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7620690	0.81[EUR][1000 genomes]
rs7626551	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7630552	0.81[EUR][1000 genomes]
rs9682464	0.95[JPT][hapmap]
rs9810807	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9823697	0.90[GIH][hapmap];0.82[YRI][hapmap]
rs9825230	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9836499	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]
rs9839035	0.86[ASN][1000 genomes]
rs9844736	0.81[JPT][hapmap]
rs9850563	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9865248	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs9866243	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9871175	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9876403	0.87[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs9880619	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9880978	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9985365	0.92[CEU][hapmap];0.86[JPT][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[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:10)

SNP	Gene	Cis/trans	Tissue	Source
rs9860296	ITIH4	cis	cerebellum	SCAN
rs9860296	ITIH4-AS1	cis	lung	GTEx
rs9860296	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs9860296	ITIH4-AS1	cis	Artery Tibial	GTEx
rs9860296	GNL3	cis	parietal	SCAN
rs9860296	SEMA3G	cis	parietal	SCAN
rs9860296	TEX264	cis	parietal	SCAN
rs9860296	GNL3	cis	cerebellum	SCAN
rs9860296	TMEM110	cis	multi-tissue	Pritchard
rs9860296	ITIH4	cis	lymphoblastoid	seeQTL

Chromatin state (count:103 , 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	chr3:52887000-52919400	Weak transcription	Fetal Brain Female	brain
4	chr3:52887000-52926400	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:52887800-52923200	Weak transcription	Brain Germinal Matrix	brain
6	chr3:52891600-52919600	Weak transcription	Left Ventricle	heart
7	chr3:52892000-52926400	Weak transcription	Rectal Smooth Muscle	rectum
8	chr3:52895400-52919400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr3:52895800-52923800	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:52895800-52925200	Weak transcription	Esophagus	oesophagus
11	chr3:52902200-52925200	Weak transcription	Placenta	Placenta
12	chr3:52904000-52918400	Weak transcription	Fetal Intestine Large	intestine
13	chr3:52904600-52919400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr3:52905000-52919800	Weak transcription	Right Ventricle	heart
15	chr3:52906000-52924400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
16	chr3:52908000-52915800	Weak transcription	Colon Smooth Muscle	Colon
17	chr3:52908000-52916200	Weak transcription	Aorta	Aorta
18	chr3:52908000-52924000	Weak transcription	Brain Hippocampus Middle	brain
19	chr3:52908000-52924000	Weak transcription	Brain Substantia Nigra	brain
20	chr3:52908200-52919000	Weak transcription	NHEK	skin
21	chr3:52908200-52919600	Weak transcription	HSMM	muscle
22	chr3:52908200-52925400	Weak transcription	Brain Anterior Caudate	brain
23	chr3:52908200-52925400	Weak transcription	Duodenum Smooth Muscle	Duodenum
24	chr3:52908400-52924400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr3:52908400-52924600	Weak transcription	NHLF	lung
26	chr3:52908400-52930600	Weak transcription	A549	lung
27	chr3:52908600-52916800	Weak transcription	Osteobl	bone
28	chr3:52908600-52924600	Weak transcription	Muscle Satellite Cultured Cells	--
29	chr3:52908600-52926000	Weak transcription	Pancreatic Islets	Pancreatic Islet
30	chr3:52909200-52919400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:52909200-52920000	Weak transcription	Liver	Liver
32	chr3:52909200-52925200	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:52909600-52925400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr3:52909800-52915800	Weak transcription	Primary T cells from cord blood	blood
35	chr3:52909800-52925200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:52909800-52925400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
37	chr3:52910000-52914200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr3:52910000-52916200	Weak transcription	Psoas Muscle	Psoas
39	chr3:52910000-52918800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr3:52910000-52919400	Weak transcription	Dnd41	blood
41	chr3:52910000-52929400	Weak transcription	HMEC	breast
42	chr3:52910000-52930200	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr3:52910200-52920200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr3:52910200-52925400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
45	chr3:52910200-52929800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr3:52910200-52930000	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr3:52910200-52930000	Weak transcription	HUES64 Cell Line	embryonic stem cell
48	chr3:52910200-52930000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
49	chr3:52910400-52914000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
50	chr3:52910400-52916000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links