Variant report

Variant	rs2240915
Chromosome Location	chr3:52859526-52859527
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52834279..52837211-chr3:52858122..52860407,2	K562	blood:

Variant related genes	Relation type
ENSG00000162267	Chromatin interaction

Extended variants
information (count: 69 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11130331	0.87[CEU][hapmap]
rs11715347	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11719137	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11915546	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11918800	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11922961	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11922975	0.91[CEU][hapmap]
rs12492391	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs13072536	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs13083728	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs1573815	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2071042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2239547	0.86[CHB][hapmap];0.90[JPT][hapmap]
rs2239548	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2240917	0.91[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245538	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2245647	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2256332	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2276815	0.86[JPT][hapmap]
rs2276817	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2276823	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2276825	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs2336558	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2336668	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs2535627	0.90[YRI][hapmap]
rs2535633	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733047	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs3774364	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3821873	0.92[CEU][hapmap];0.87[CHB][hapmap]
rs4302374	0.82[JPT][hapmap]
rs4687554	0.82[CHB][hapmap];0.90[JPT][hapmap]
rs4687657	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs4687658	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs4687663	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs4687672	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs4687680	0.92[CEU][hapmap];0.87[CHB][hapmap];0.82[JPT][hapmap]
rs4687682	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs4687687	0.91[CEU][hapmap]
rs56019197	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60332615	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6445538	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6445539	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs6445541	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6445547	0.82[JPT][hapmap]
rs6769789	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs6803519	0.83[CHB][hapmap];0.90[JPT][hapmap]
rs7612624	0.82[ASN][1000 genomes]
rs7617468	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7620690	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7626551	0.88[CEU][hapmap]
rs7630552	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs7652667	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9682464	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs9810807	0.91[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs9836499	0.92[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap]
rs9850563	0.92[CEU][hapmap];0.91[CHB][hapmap];0.82[JPT][hapmap]
rs9860296	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap]
rs9876403	0.85[JPT][hapmap]
rs9880978	0.96[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs9985365	0.84[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv984563	chr3:52516115-52867075	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	nsv590308	chr3:52854335-52860806	Strong transcription Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
8	nsv876798	chr3:52856609-52863133	Weak transcription Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2240915	ITIH4	cis	multi-tissue	Pritchard
rs2240915	ITIH4	cis	Lymphoblastoid	GTEx
rs2240915	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs2240915	ITIH4-AS1	cis	Artery Aorta	GTEx
rs2240915	ITIH4-AS1	cis	lung	GTEx
rs2240915	ITIH4-AS1	cis	Muscle Skeletal	GTEx
rs2240915	FLJ12442	cis	multi-tissue	Pritchard
rs2240915	ITIH4-AS1	cis	Artery Tibial	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52846400-52860800	Weak transcription	Esophagus	oesophagus
2	chr3:52847200-52861200	Genic enhancers	Liver	Liver
3	chr3:52847600-52865000	Weak transcription	Psoas Muscle	Psoas
4	chr3:52848400-52865800	Weak transcription	Ovary	ovary
5	chr3:52850200-52868400	Weak transcription	Colonic Mucosa	Colon
6	chr3:52850600-52864200	Strong transcription	Stomach Smooth Muscle	stomach
7	chr3:52850800-52865400	Strong transcription	Fetal Stomach	stomach
8	chr3:52851600-52863400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
9	chr3:52852200-52869200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
10	chr3:52852800-52869200	Weak transcription	Primary B cells from cord blood	blood
11	chr3:52853000-52868000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr3:52853400-52861200	Strong transcription	Fetal Muscle Leg	muscle
13	chr3:52854000-52861200	Strong transcription	Pancreas	Pancrea
14	chr3:52854200-52874200	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr3:52854400-52861600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr3:52854800-52869200	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:52854800-52888400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr3:52855000-52861600	Strong transcription	Skeletal Muscle Female	skeletal muscle
19	chr3:52855200-52860800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr3:52855200-52865400	Weak transcription	Brain Substantia Nigra	brain
21	chr3:52855600-52862000	Strong transcription	Skeletal Muscle Male	skeletal muscle
22	chr3:52855600-52865400	Weak transcription	Colon Smooth Muscle	Colon
23	chr3:52856000-52865400	Weak transcription	Rectal Smooth Muscle	rectum
24	chr3:52856000-52875000	Weak transcription	Fetal Intestine Large	intestine
25	chr3:52856200-52865600	Weak transcription	Left Ventricle	heart
26	chr3:52856400-52868200	Weak transcription	Fetal Lung	lung
27	chr3:52856600-52860400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr3:52856600-52861000	Strong transcription	Fetal Muscle Trunk	muscle
29	chr3:52856600-52861200	Strong transcription	Primary T cells from cord blood	blood
30	chr3:52856600-52864400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr3:52856800-52863400	Strong transcription	Fetal Thymus	thymus
32	chr3:52857000-52861000	Weak transcription	HepG2	liver
33	chr3:52857000-52868600	Weak transcription	Primary B cells from peripheral blood	blood
34	chr3:52857800-52865400	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr3:52858000-52867800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr3:52858000-52868400	Weak transcription	Brain Germinal Matrix	brain
37	chr3:52858200-52865400	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr3:52858400-52861400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr3:52858400-52865400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:52858400-52865400	Weak transcription	Brain Angular Gyrus	brain
41	chr3:52858400-52866800	Weak transcription	Fetal Brain Female	brain
42	chr3:52858400-52867200	Weak transcription	Primary T cells fromperipheralblood	blood
43	chr3:52858400-52867600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
44	chr3:52858600-52861000	Weak transcription	Spleen	Spleen
45	chr3:52858600-52861800	Weak transcription	Gastric	stomach
46	chr3:52858600-52864600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr3:52858600-52864800	Weak transcription	Right Ventricle	heart
48	chr3:52858600-52865600	Weak transcription	Brain Hippocampus Middle	brain
49	chr3:52858600-52866800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:52858600-52867000	Weak transcription	Primary monocytes fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links