Variant report

Variant	rs782980
Chromosome Location	chr5:43177325-43177326
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10072230	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11742417	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11743970	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11744749	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11748554	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1617756	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1622767	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17242550	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs17242918	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2330086	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2444780	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444781	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2444782	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28845781	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs496570	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs497982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506244	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs514567	1.00[YRI][hapmap];0.87[AFR][1000 genomes]
rs524985	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs546194	0.95[AFR][1000 genomes]
rs60289145	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73751050	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7719222	0.97[AFR][1000 genomes];0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv993554	chr5:42720939-43251863	Bivalent/Poised TSS Strong transcription Active TSS Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	298 gene(s)	inside rSNPs	diseases
2	nsv462126	chr5:42728831-43237188	Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
3	nsv597925	chr5:42728831-43237188	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	297 gene(s)	inside rSNPs	diseases
4	nsv1023741	chr5:42768215-43348145	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
5	nsv537737	chr5:42768215-43348145	Genic enhancers Enhancers Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	309 gene(s)	inside rSNPs	diseases
6	nsv1024636	chr5:42959979-43295782	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
7	nsv537739	chr5:42959979-43295782	Strong transcription Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	283 gene(s)	inside rSNPs	diseases
8	nsv830274	chr5:43095551-43226087	Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	138 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:43124000-43183000	Weak transcription	Small Intestine	intestine
2	chr5:43127600-43178000	Strong transcription	Dnd41	blood
3	chr5:43143400-43178200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr5:43156000-43178200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr5:43156600-43191200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:43156800-43177600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr5:43157000-43178400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr5:43162000-43191600	Weak transcription	Fetal Brain Male	brain
9	chr5:43163800-43191800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr5:43164400-43191200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
11	chr5:43165000-43191200	Weak transcription	Colon Smooth Muscle	Colon
12	chr5:43169200-43179200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr5:43170000-43178000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
14	chr5:43170200-43178000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr5:43170600-43178000	Strong transcription	Primary T cells from cord blood	blood
16	chr5:43171200-43178000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr5:43171200-43178000	Strong transcription	Fetal Thymus	thymus
18	chr5:43171400-43178000	Strong transcription	Hela-S3	cervix
19	chr5:43171400-43178200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr5:43171400-43178200	Strong transcription	Fetal Muscle Leg	muscle
21	chr5:43172200-43177800	Strong transcription	Monocytes-CD14+_RO01746	blood
22	chr5:43172200-43178400	Strong transcription	Liver	Liver
23	chr5:43172200-43178800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr5:43172800-43177400	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr5:43173000-43177400	Strong transcription	A549	lung
26	chr5:43173000-43177800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr5:43173400-43177800	Strong transcription	Primary T helper cells PMA-I stimulated	--
28	chr5:43173400-43178000	Strong transcription	Skeletal Muscle Female	skeletal muscle
29	chr5:43173600-43179400	Weak transcription	NHEK	skin
30	chr5:43174400-43177800	Strong transcription	HUVEC	blood vessel
31	chr5:43175000-43179200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
32	chr5:43175000-43180400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr5:43175000-43180800	Weak transcription	Colonic Mucosa	Colon
34	chr5:43175000-43191800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
35	chr5:43175200-43177400	Weak transcription	Right Ventricle	heart
36	chr5:43175200-43177400	Weak transcription	HepG2	liver
37	chr5:43175200-43177600	Weak transcription	Fetal Stomach	stomach
38	chr5:43175200-43177600	Weak transcription	Thymus	Thymus
39	chr5:43175200-43177800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr5:43175200-43177800	Weak transcription	Esophagus	oesophagus
41	chr5:43175200-43178000	Weak transcription	Brain Hippocampus Middle	brain
42	chr5:43175200-43178400	Weak transcription	Primary hematopoietic stem cells	blood
43	chr5:43175200-43179400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
44	chr5:43175200-43180000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr5:43175200-43180000	Weak transcription	Aorta	Aorta
46	chr5:43175200-43180000	Weak transcription	Osteobl	bone
47	chr5:43175200-43180400	Weak transcription	Duodenum Mucosa	Duodenum
48	chr5:43175200-43180600	Weak transcription	Lung	lung
49	chr5:43175200-43180800	Weak transcription	Primary neutrophils fromperipheralblood	blood
50	chr5:43175200-43180800	Weak transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links