Variant report

Variant	rs7626551
Chromosome Location	chr3:52938092-52938093
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:52935990..52938094-chr3:53078849..53080891,2	K562	blood:

Variant related genes	Relation type
ENSG00000163935	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10865977	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11130331	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11918800	0.92[CEU][hapmap]
rs11922961	0.92[CEU][hapmap]
rs11922975	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12487379	0.85[EUR][1000 genomes]
rs12492391	0.96[CEU][hapmap];0.91[JPT][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12629687	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12638968	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs13072536	0.81[JPT][hapmap]
rs13072537	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13083728	0.86[JPT][hapmap]
rs1573815	0.86[JPT][hapmap]
rs2071042	0.92[CEU][hapmap]
rs2239547	0.86[JPT][hapmap]
rs2240915	0.88[CEU][hapmap]
rs2245424	0.81[CEU][hapmap]
rs2257216	0.80[CEU][hapmap];0.93[YRI][hapmap]
rs2276815	0.86[JPT][hapmap]
rs2276817	0.86[JPT][hapmap]
rs2276825	0.86[JPT][hapmap]
rs2336664	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2336667	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336668	0.96[CEU][hapmap];0.91[JPT][hapmap];0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2336670	0.82[CEU][hapmap];0.90[YRI][hapmap]
rs2535633	0.92[CEU][hapmap]
rs2710314	0.81[CEU][hapmap]
rs3733047	0.86[JPT][hapmap]
rs3821873	0.96[CEU][hapmap];0.88[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4302374	0.91[JPT][hapmap]
rs4350911	0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4687554	0.86[JPT][hapmap]
rs4687562	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4687657	0.86[JPT][hapmap]
rs4687658	0.86[JPT][hapmap]
rs4687663	0.81[JPT][hapmap]
rs4687672	0.86[JPT][hapmap]
rs4687679	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4687680	0.96[CEU][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4687682	0.96[CEU][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687683	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687684	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4687687	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4687689	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56383738	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62253583	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6445538	0.86[JPT][hapmap]
rs6445539	0.86[JPT][hapmap]
rs6445541	0.88[CEU][hapmap]
rs6445547	0.91[JPT][hapmap]
rs6764322	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6769789	0.92[CEU][hapmap]
rs6773650	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6795646	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6799185	0.80[CEU][hapmap]
rs6803519	0.86[JPT][hapmap]
rs7612624	0.81[AMR][1000 genomes]
rs9682464	0.86[JPT][hapmap]
rs9810807	0.95[CEU][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9823697	0.80[CEU][hapmap];0.93[YRI][hapmap]
rs9825230	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9836499	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]
rs9844736	0.95[JPT][hapmap]
rs9850563	0.96[CEU][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9860296	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]
rs9865248	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9866243	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9871175	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9876403	0.90[JPT][hapmap]
rs9880619	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9880978	0.96[CEU][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9985365	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
rs7626551	ITIH4-AS1	cis	lung	GTEx
rs7626551	NT5DC2	Cis_1M	lymphoblastoid	RTeQTL
rs7626551	ITIH4-AS1	cis	Artery Tibial	GTEx
rs7626551	ITIH4-AS1	cis	Artery Aorta	GTEx

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:52931600-52945000	Weak transcription	Gastric	stomach
2	chr3:52931800-52965400	Weak transcription	Spleen	Spleen
3	chr3:52932000-52938200	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr3:52932000-52938600	Weak transcription	Left Ventricle	heart
5	chr3:52932000-52938800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:52932000-52939000	Weak transcription	Aorta	Aorta
7	chr3:52932000-52939000	Weak transcription	Psoas Muscle	Psoas
8	chr3:52932000-52940000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr3:52932000-52941000	Weak transcription	Lung	lung
10	chr3:52932000-52943600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:52932000-52943800	Weak transcription	Pancreas	Pancrea
12	chr3:52932000-52946400	Weak transcription	Esophagus	oesophagus
13	chr3:52932000-52953400	Weak transcription	Rectal Smooth Muscle	rectum
14	chr3:52932000-52954000	Weak transcription	Small Intestine	intestine
15	chr3:52932000-52964000	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr3:52932000-52970000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr3:52932000-52978000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr3:52932200-52938200	Weak transcription	Fetal Intestine Small	intestine
19	chr3:52932200-52938800	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:52932200-52939000	Weak transcription	GM12878-XiMat	blood
21	chr3:52932200-52939400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
22	chr3:52932200-52940000	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr3:52932200-52940200	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr3:52932200-52940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr3:52932200-52940800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr3:52932200-52941000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
27	chr3:52932200-52946000	Weak transcription	Colon Smooth Muscle	Colon
28	chr3:52932200-52948600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr3:52932200-52948800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr3:52932200-52951400	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr3:52932200-52952800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr3:52932200-52953600	Weak transcription	Right Ventricle	heart
33	chr3:52932200-52953800	Weak transcription	Ovary	ovary
34	chr3:52932200-52961400	Weak transcription	HSMMtube	muscle
35	chr3:52932200-52961800	Weak transcription	A549	lung
36	chr3:52932200-52963000	Weak transcription	Stomach Mucosa	stomach
37	chr3:52932200-52966400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr3:52932200-52967800	Weak transcription	HSMM	muscle
39	chr3:52932200-52968600	Weak transcription	Osteobl	bone
40	chr3:52932200-52968800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr3:52932200-52968800	Weak transcription	Fetal Brain Male	brain
42	chr3:52932400-52938200	Weak transcription	Brain Substantia Nigra	brain
43	chr3:52932400-52938200	Weak transcription	Fetal Lung	lung
44	chr3:52932400-52938600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:52932400-52938600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr3:52932400-52938600	Weak transcription	Fetal Muscle Leg	muscle
47	chr3:52932400-52938600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr3:52932400-52938800	Weak transcription	Brain Germinal Matrix	brain
49	chr3:52932400-52938800	Weak transcription	Hela-S3	cervix
50	chr3:52932400-52939000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links