Variant report

Variant	rs873787
Chromosome Location	chr5:75843577-75843578
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 38 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10462543	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11948805	0.86[JPT][hapmap]
rs12513400	1.00[CEU][hapmap];0.95[CHB][hapmap];0.86[JPT][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12513594	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12513678	0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12519094	0.91[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs12519329	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12519473	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12521026	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12523647	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1501788	0.95[JPT][hapmap]
rs1566	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17680732	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17680756	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17680811	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17748322	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs3736394	0.95[JPT][hapmap]
rs3756514	1.00[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];0.86[JPT][hapmap];0.94[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3797388	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[CHD][hapmap];0.92[GIH][hapmap];0.82[JPT][hapmap];0.81[MEX][hapmap]
rs3912001	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4703713	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4704329	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4704340	0.81[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs55699952	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56338424	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58087114	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60881227	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61014011	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs61233297	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs869733	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs879017	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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	nsv1022032	chr5:75785106-75914003	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer 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	3 gene(s)	inside rSNPs	diseases
2	nsv598679	chr5:75823965-75914729	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1023953	chr5:75831037-75913784	Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1026257	chr5:75831037-75914003	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv1016823	chr5:75831037-75915905	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1019669	chr5:75836365-76477788	Weak transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
7	nsv598680	chr5:75839165-75914729	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS 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	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:75835600-75871200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr5:75839600-75845400	Enhancers	HepG2	liver
3	chr5:75839600-75845800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
4	chr5:75839600-75846000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr5:75840400-75843600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr5:75842000-75843800	Enhancers	Fetal Muscle Leg	muscle
7	chr5:75842000-75844600	Enhancers	Primary B cells from peripheral blood	blood
8	chr5:75842000-75845800	Enhancers	Stomach Mucosa	stomach
9	chr5:75842200-75843600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:75842200-75843600	Enhancers	Pancreas	Pancrea
11	chr5:75842200-75843800	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr5:75842200-75844200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
13	chr5:75842200-75844400	Enhancers	Fetal Thymus	thymus
14	chr5:75842200-75844600	Flanking Active TSS	GM12878-XiMat	blood
15	chr5:75842200-75844800	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
16	chr5:75842200-75845800	Enhancers	Sigmoid Colon	Sigmoid Colon
17	chr5:75842400-75843600	Enhancers	K562	blood
18	chr5:75842400-75843800	Enhancers	H9 Cell Line	embryonic stem cell
19	chr5:75842400-75843800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr5:75842400-75843800	Enhancers	Fetal Kidney	kidney
21	chr5:75842400-75844000	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr5:75842400-75844000	Weak transcription	Skeletal Muscle Female	skeletal muscle
23	chr5:75842400-75844200	Enhancers	Fetal Stomach	stomach
24	chr5:75842400-75844400	Enhancers	Placenta	Placenta
25	chr5:75842400-75844800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr5:75842400-75844800	Enhancers	Small Intestine	intestine
27	chr5:75842400-75845000	Enhancers	Fetal Intestine Small	intestine
28	chr5:75842400-75845600	Enhancers	Gastric	stomach
29	chr5:75842600-75843800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr5:75842600-75843800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr5:75842600-75844800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr5:75842600-75845000	Enhancers	Fetal Lung	lung
33	chr5:75842600-75851600	Weak transcription	Esophagus	oesophagus
34	chr5:75842800-75843600	Flanking Active TSS	Primary T cells from cord blood	blood
35	chr5:75842800-75843600	Flanking Active TSS	Liver	Liver
36	chr5:75842800-75843800	Flanking Active TSS	Primary T cells fromperipheralblood	blood
37	chr5:75842800-75843800	Flanking Active TSS	Primary hematopoietic stem cells	blood
38	chr5:75842800-75843800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
39	chr5:75842800-75843800	Flanking Active TSS	Duodenum Mucosa	Duodenum
40	chr5:75842800-75844200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr5:75842800-75844600	Weak transcription	Colonic Mucosa	Colon
42	chr5:75842800-75845200	Weak transcription	Spleen	Spleen
43	chr5:75843000-75843600	Enhancers	Dnd41	blood
44	chr5:75843000-75843800	Enhancers	Fetal Intestine Large	intestine
45	chr5:75843000-75844200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
46	chr5:75843000-75844400	Enhancers	iPS-18 Cell Line	embryonic stem cell
47	chr5:75843000-75844400	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr5:75843200-75843600	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr5:75843200-75843600	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr5:75843200-75843600	Active TSS	Primary B cells from cord blood	blood

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