Variant report

Variant	rs13225672
Chromosome Location	chr7:65680248-65680249
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 86 )
Associated
traits (count: 17 )

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

rs_ID	r²[population]
rs1000464	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs10224872	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10228885	0.82[EUR][1000 genomes]
rs10240949	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10250544	0.84[EUR][1000 genomes]
rs10255397	0.83[EUR][1000 genomes]
rs10256544	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10257911	0.82[EUR][1000 genomes]
rs10260426	0.83[EUR][1000 genomes]
rs10261398	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10263690	0.83[EUR][1000 genomes]
rs10272149	0.86[EUR][1000 genomes]
rs10276077	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10282433	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10447522	0.83[EUR][1000 genomes]
rs10950033	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11760844	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11769079	0.81[EUR][1000 genomes]
rs11984115	0.82[EUR][1000 genomes]
rs12531677	0.83[EUR][1000 genomes]
rs12534500	0.85[EUR][1000 genomes]
rs12537823	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13230545	0.83[EUR][1000 genomes]
rs13309935	0.89[EUR][1000 genomes]
rs1532571	0.83[EUR][1000 genomes]
rs1875057	0.83[EUR][1000 genomes]
rs2036263	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2088653	0.82[EUR][1000 genomes]
rs2088655	0.83[EUR][1000 genomes]
rs2420173	0.80[EUR][1000 genomes]
rs2420174	0.80[EUR][1000 genomes]
rs28491091	0.85[EUR][1000 genomes]
rs2901152	0.82[EUR][1000 genomes]
rs34913718	0.85[EUR][1000 genomes]
rs4078376	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4149461	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4236208	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4587224	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4718319	0.80[EUR][1000 genomes]
rs4718324	0.85[EUR][1000 genomes]
rs4718328	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4718329	0.84[EUR][1000 genomes]
rs4718330	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6460278	0.85[EUR][1000 genomes]
rs6460279	0.85[EUR][1000 genomes]
rs6460282	0.86[EUR][1000 genomes]
rs6460284	0.83[EUR][1000 genomes]
rs6460287	0.82[EUR][1000 genomes]
rs6460290	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6460293	0.82[EUR][1000 genomes]
rs6944374	0.86[EUR][1000 genomes]
rs6951503	0.83[EUR][1000 genomes]
rs6952182	0.86[EUR][1000 genomes]
rs6952473	0.81[EUR][1000 genomes]
rs6958294	0.83[EUR][1000 genomes]
rs6959268	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs6960446	0.83[EUR][1000 genomes]
rs6964437	0.86[EUR][1000 genomes]
rs6967708	0.80[EUR][1000 genomes]
rs6971752	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6974614	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6979452	0.81[EUR][1000 genomes]
rs709596	0.84[EUR][1000 genomes]
rs71526537	0.81[EUR][1000 genomes]
rs7781880	0.80[EUR][1000 genomes]
rs7782704	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7782806	0.80[EUR][1000 genomes]
rs7783779	0.83[EUR][1000 genomes]
rs778680	0.84[EUR][1000 genomes]
rs778684	0.85[EUR][1000 genomes]
rs778686	0.85[EUR][1000 genomes]
rs778724	0.85[EUR][1000 genomes]
rs778728	0.82[EUR][1000 genomes]
rs778734	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs778736	0.82[EUR][1000 genomes]
rs7787482	0.87[EUR][1000 genomes]
rs7796162	0.82[EUR][1000 genomes]
rs7798630	0.83[EUR][1000 genomes]
rs880166	0.89[EUR][1000 genomes]
rs949930	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2761079	chr7:65092426-65689733	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv532124	chr7:65371521-66234730	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
3	nsv1026559	chr7:65617368-66370805	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv1028692	chr7:65673136-65751069	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv538908	chr7:65673136-65751069	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	esv3389228	chr7:65679117-65681065	Weak transcription Enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:17)

SNP	Gene	Cis/trans	Tissue	Source
rs13225672	RP4-756H11.3	cis	Artery Tibial	GTEx
rs13225672	RNU6-96P	cis	Thyroid	GTEx
rs13225672	GS1-124K5.4	cis	Esophagus Mucosa	GTEx
rs13225672	RP4-756H11.3	cis	Muscle Skeletal	GTEx
rs13225672	ASL	Cis_1M	lymphoblastoid	RTeQTL
rs13225672	GTF2IRD1P1	cis	Thyroid	GTEx
rs13225672	RP4-756H11.3	cis	Skin Sun Exposed Lower leg	GTEx
rs13225672	RP4-756H11.3	cis	lung	GTEx
rs13225672	RP4-756H11.3	cis	Adipose Subcutaneous	GTEx
rs13225672	RP4-756H11.3	cis	Nerve Tibial	GTEx
rs13225672	RP4-756H11.3	cis	Esophagus Muscularis	GTEx
rs13225672	GS1-124K5.11	cis	Thyroid	GTEx
rs13225672	RP4-756H11.3	cis	Heart Left Ventricle	GTEx
rs13225672	GS1-124K5.4	cis	Skin Sun Exposed Lower leg	GTEx
rs13225672	RP4-756H11.3	cis	Thyroid	GTEx
rs13225672	LINC00174	cis	Thyroid	GTEx
rs13225672	RP4-756H11.3	cis	Esophagus Mucosa	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:65671600-65685400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:65671600-65689000	Weak transcription	Pancreas	Pancrea
3	chr7:65671800-65682200	Weak transcription	Left Ventricle	heart
4	chr7:65672200-65687400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr7:65672200-65723400	Weak transcription	Right Atrium	heart
6	chr7:65672600-65687600	Weak transcription	Brain Germinal Matrix	brain
7	chr7:65673000-65689000	Weak transcription	HMEC	breast
8	chr7:65673400-65689000	Weak transcription	Brain Hippocampus Middle	brain
9	chr7:65673600-65682800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr7:65674000-65688800	Weak transcription	Ovary	ovary
11	chr7:65675600-65685400	Weak transcription	Esophagus	oesophagus
12	chr7:65676000-65681000	Weak transcription	Liver	Liver
13	chr7:65676000-65684400	Weak transcription	HepG2	liver
14	chr7:65676000-65689000	Weak transcription	Lung	lung
15	chr7:65676000-65696200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr7:65676000-65716800	Weak transcription	Primary B cells from cord blood	blood
17	chr7:65676200-65696200	Weak transcription	Fetal Stomach	stomach
18	chr7:65676600-65691200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr7:65676600-65693200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr7:65676800-65685400	Weak transcription	Gastric	stomach
21	chr7:65677000-65694600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr7:65677200-65693800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr7:65677800-65688800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr7:65679000-65683600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr7:65679200-65681600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr7:65679200-65684200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
27	chr7:65679200-65685400	Weak transcription	NHDF-Ad	bronchial
28	chr7:65679200-65686200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr7:65679200-65686200	Weak transcription	Osteobl	bone
30	chr7:65679200-65686600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr7:65679200-65686600	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr7:65679200-65687600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr7:65679200-65688600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr7:65679800-65683200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links