Variant report

Variant	rs10479520
Chromosome Location	chr5:178451447-178451448
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:58)

rs_ID	r²[population]
rs10479519	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10516149	0.95[ASN][1000 genomes]
rs10516150	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11505147	0.82[ASN][1000 genomes]
rs11951738	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11957976	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11958355	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11960161	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12152869	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13160086	0.86[ASN][1000 genomes]
rs13161528	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13188724	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13359549	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359570	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13359572	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13361077	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17078988	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17078991	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2047354	0.82[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132671	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2132672	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34054398	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34431447	0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34881171	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35568336	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3797615	0.86[ASN][1000 genomes]
rs4700780	0.94[ASN][1000 genomes]
rs4700781	0.88[ASN][1000 genomes]
rs4701030	0.95[ASN][1000 genomes]
rs4701045	0.88[ASN][1000 genomes]
rs58827878	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60061283	0.90[ASN][1000 genomes]
rs60073676	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62393072	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393074	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62393075	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62393076	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6601007	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6601010	0.85[ASN][1000 genomes]
rs6859576	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6859767	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6860309	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6861539	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6867119	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6867208	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6868893	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6875473	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6875622	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6880315	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6888539	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6888567	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6890317	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7707587	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7708743	0.92[ASN][1000 genomes]
rs7709054	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7711420	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7732719	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7733072	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv883219	chr5:178390237-178454118	Enhancers ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv883220	chr5:178394717-178454118	ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv883221	chr5:178410538-178454118	Weak transcription Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1024560	chr5:178415364-178917595	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv537975	chr5:178415364-178917595	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv817413	chr5:178415365-179020558	Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
7	nsv1033597	chr5:178423101-178752095	Strong transcription Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1018650	chr5:178428743-178515196	Weak transcription ZNF genes & repeats Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
9	nsv1024994	chr5:178429975-178505167	Active TSS Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
10	nsv1025616	chr5:178429975-178515196	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
11	nsv1026351	chr5:178429975-178535309	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
12	nsv1031829	chr5:178442633-178658706	Strong transcription Weak transcription ZNF genes & repeats Bivalent Enhancer Enhancers Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10479520	DKFZp686E2433	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:178449600-178451600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr5:178449800-178451600	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr5:178449800-178451600	Active TSS	H1 Cell Line	embryonic stem cell
4	chr5:178449800-178451600	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr5:178449800-178451600	Active TSS	Duodenum Smooth Muscle	Duodenum
6	chr5:178449800-178451800	Active TSS	HMEC	breast
7	chr5:178449800-178452000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr5:178449800-178452000	Active TSS	Psoas Muscle	Psoas
9	chr5:178450000-178451600	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr5:178450000-178451600	Active TSS	Pancreatic Islets	Pancreatic Islet
11	chr5:178450000-178451600	Active TSS	Fetal Stomach	stomach
12	chr5:178450000-178451600	Active TSS	Right Atrium	heart
13	chr5:178450000-178451800	Active TSS	H9 Cell Line	embryonic stem cell
14	chr5:178450000-178452200	Active TSS	Duodenum Mucosa	Duodenum
15	chr5:178450000-178452200	Active TSS	Fetal Kidney	kidney
16	chr5:178450200-178451600	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr5:178450200-178451600	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr5:178450200-178451600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr5:178450200-178451600	Active TSS	Muscle Satellite Cultured Cells	--
20	chr5:178450200-178451600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr5:178450200-178451600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr5:178450200-178451600	Active TSS	Aorta	Aorta
23	chr5:178450200-178451600	Active TSS	Brain Cingulate Gyrus	brain
24	chr5:178450200-178451600	Active TSS	Colonic Mucosa	Colon
25	chr5:178450200-178451600	Active TSS	Fetal Intestine Large	intestine
26	chr5:178450200-178451600	Active TSS	Lung	lung
27	chr5:178450200-178451600	Active TSS	Rectal Mucosa Donor 31	rectum
28	chr5:178450200-178451600	Active TSS	Right Ventricle	heart
29	chr5:178450200-178451600	Active TSS	Thymus	Thymus
30	chr5:178450200-178451600	Active TSS	A549	lung
31	chr5:178450200-178451600	Active TSS	HSMM	muscle
32	chr5:178450200-178451600	Active TSS	NH-A	brain
33	chr5:178450200-178451600	Active TSS	NHDF-Ad	bronchial
34	chr5:178450200-178451800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
35	chr5:178450200-178451800	Active TSS	HUES48 Cell Line	embryonic stem cell
36	chr5:178450200-178451800	Active TSS	HUES6 Cell Line	embryonic stem cell
37	chr5:178450200-178451800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
38	chr5:178450200-178451800	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr5:178450200-178451800	Active TSS	HSMMtube	muscle
40	chr5:178450200-178451800	Active TSS	NHLF	lung
41	chr5:178450200-178452000	Active TSS	Rectal Mucosa Donor 29	rectum
42	chr5:178450400-178451600	Active TSS	Ovary	ovary
43	chr5:178450600-178451600	Active TSS	Fetal Muscle Trunk	muscle
44	chr5:178450800-178451600	Flanking Active TSS	Primary B cells from cord blood	blood
45	chr5:178451000-178451600	Flanking Active TSS	Primary hematopoietic stem cells	blood
46	chr5:178451000-178451600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
47	chr5:178451000-178451600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
48	chr5:178451000-178451600	Enhancers	K562	blood
49	chr5:178451000-178451800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr5:178451000-178451800	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links