Variant report

Variant	rs1126643
Chromosome Location	chr5:52347369-52347370
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1062535	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12515364	0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12517446	0.82[ASN][1000 genomes]
rs12518279	0.88[ASN][1000 genomes]
rs12521915	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12652168	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1421929	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1421930	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1421931	0.81[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1421932	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1833558	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1862191	0.87[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs1991013	0.88[ASN][1000 genomes]
rs2075615	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2075616	0.82[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2075617	0.82[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2287871	0.87[ASN][1000 genomes]
rs2303122	0.94[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.87[YRI][hapmap];0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2303123	0.90[ASN][1000 genomes]
rs2303127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2897458	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910964	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2910965	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2910971	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2974976	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2974978	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2974987	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212467	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3212472	0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3212508	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212509	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3212522	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212527	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212533	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3212591	0.88[ASN][1000 genomes]
rs3212600	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3212601	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3212619	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3212640	0.83[ASN][1000 genomes]
rs3797495	0.87[YRI][hapmap]
rs3797498	0.91[YRI][hapmap]
rs67719154	0.86[AFR][1000 genomes];0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs6880055	0.87[YRI][hapmap]
rs6898333	1.00[CHB][hapmap];0.82[JPT][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7725246	0.93[ASW][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.97[LWK][hapmap];0.87[MEX][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs984966	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs989073	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs990602	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949005	chr5:52188028-52808229	Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv830296	chr5:52209528-52410253	Strong transcription Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
3	nsv881652	chr5:52323568-52385312	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv880389	chr5:52333420-52375199	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
5	nsv881071	chr5:52334774-52362765	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	nsv881388	chr5:52339234-52375536	Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv880600	chr5:52342760-52362765	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1126643	SNX18	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:52314200-52348000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr5:52324400-52356400	Weak transcription	Brain Anterior Caudate	brain
3	chr5:52328000-52369200	Weak transcription	Fetal Intestine Small	intestine
4	chr5:52328800-52348000	Weak transcription	Fetal Intestine Large	intestine
5	chr5:52333800-52348800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr5:52333800-52369800	Weak transcription	Colonic Mucosa	Colon
7	chr5:52333800-52392600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr5:52334000-52360800	Weak transcription	Small Intestine	intestine
9	chr5:52334400-52348000	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:52334600-52348400	Weak transcription	Lung	lung
11	chr5:52334800-52348000	Weak transcription	Brain Substantia Nigra	brain
12	chr5:52334800-52380800	Weak transcription	Stomach Mucosa	stomach
13	chr5:52334800-52391200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr5:52336400-52399800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr5:52337200-52353400	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:52337400-52348800	Weak transcription	A549	lung
17	chr5:52337400-52355200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr5:52337400-52369000	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr5:52337400-52370200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr5:52338000-52348200	Weak transcription	Brain Cingulate Gyrus	brain
21	chr5:52341200-52396400	Strong transcription	HMEC	breast
22	chr5:52341400-52348600	Weak transcription	Dnd41	blood
23	chr5:52341400-52359000	Weak transcription	NHDF-Ad	bronchial
24	chr5:52341400-52396400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr5:52341800-52347800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr5:52341800-52358800	Weak transcription	Osteobl	bone
27	chr5:52342000-52367200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr5:52342400-52363600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr5:52342600-52383800	Strong transcription	NHEK	skin
30	chr5:52343000-52348600	Weak transcription	Fetal Muscle Leg	muscle
31	chr5:52343000-52359000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr5:52343200-52350800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr5:52343200-52351800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
34	chr5:52343200-52361800	Strong transcription	HepG2	liver
35	chr5:52343400-52350000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr5:52343400-52357200	Strong transcription	HUVEC	blood vessel
37	chr5:52343400-52392800	Weak transcription	Left Ventricle	heart
38	chr5:52343600-52348000	Weak transcription	Spleen	Spleen
39	chr5:52344000-52348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr5:52344000-52369200	Weak transcription	Pancreas	Pancrea
41	chr5:52344200-52356000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr5:52344400-52348000	Weak transcription	Brain Hippocampus Middle	brain
43	chr5:52344400-52348200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
44	chr5:52344400-52356400	Weak transcription	Esophagus	oesophagus
45	chr5:52344400-52356400	Weak transcription	Gastric	stomach
46	chr5:52345600-52350800	Strong transcription	Hela-S3	cervix
47	chr5:52346200-52349000	Weak transcription	Fetal Brain Male	brain
48	chr5:52346200-52386800	Weak transcription	Stomach Smooth Muscle	stomach
49	chr5:52346400-52347600	Strong transcription	Muscle Satellite Cultured Cells	--
50	chr5:52346400-52348000	Weak transcription	Primary hematopoietic stem cells short term culture	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links