Variant report

Variant	rs13185634
Chromosome Location	chr5:49707628-49707629
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 48 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs13154127	0.80[EUR][1000 genomes]
rs13154421	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13158256	1.00[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs13160401	1.00[AFR][1000 genomes]
rs13165145	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs13169411	0.95[EUR][1000 genomes]
rs13174803	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs13189140	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17192300	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17192503	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17800685	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[GIH][hapmap];0.81[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1962207	1.00[CEU][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34107321	0.80[EUR][1000 genomes]
rs34434894	1.00[AFR][1000 genomes]
rs34573392	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs34836131	1.00[AFR][1000 genomes]
rs34982640	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs35005767	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35220247	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35290633	1.00[AFR][1000 genomes];0.80[EUR][1000 genomes]
rs35319490	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs35647517	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35703604	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35831659	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs3860733	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs61133464	0.95[EUR][1000 genomes]
rs6893317	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71631455	0.80[EUR][1000 genomes]
rs71631457	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71631459	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs71631461	1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs71631463	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs71631464	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71631467	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71631475	1.00[AFR][1000 genomes]
rs7709512	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][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	nsv1023402	chr5:49455624-49708458	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv1032003	chr5:49455624-49881491	Strong transcription Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1016583	chr5:49455624-50116720	Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv1023140	chr5:49455624-50121623	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv1023981	chr5:49584188-49871537	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv537757	chr5:49584188-49871537	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1022067	chr5:49584188-49960083	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
8	nsv537758	chr5:49584188-49960083	Active TSS Enhancers Weak transcription Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	nsv918220	chr5:49584188-50111282	Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv931010	chr5:49584189-50118254	Genic enhancers Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv916441	chr5:49584313-49831223	Active TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv523212	chr5:49597497-50058043	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13185634	LOC647121	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:49682000-49719000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
2	chr5:49688800-49710000	Weak transcription	Fetal Thymus	thymus
3	chr5:49690200-49723600	Weak transcription	Duodenum Mucosa	Duodenum
4	chr5:49690400-49708600	Strong transcription	Dnd41	blood
5	chr5:49692800-49708000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr5:49695600-49708400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr5:49697400-49723400	Weak transcription	HSMM	muscle
9	chr5:49697600-49709800	Weak transcription	Primary T cells from cord blood	blood
10	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr5:49698200-49711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr5:49701000-49711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr5:49703200-49709200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr5:49703200-49719000	Weak transcription	HMEC	breast
16	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
17	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr5:49703400-49708200	Weak transcription	Primary B cells from peripheral blood	blood
19	chr5:49703400-49711800	Weak transcription	Primary monocytes fromperipheralblood	blood
20	chr5:49703600-49708000	Weak transcription	NHEK	skin
21	chr5:49703600-49711400	Weak transcription	Monocytes-CD14+_RO01746	blood
22	chr5:49704200-49710000	Weak transcription	Fetal Intestine Small	intestine
23	chr5:49704400-49711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
24	chr5:49705200-49709200	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr5:49705200-49710600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr5:49705400-49709400	Weak transcription	Primary T cells fromperipheralblood	blood
27	chr5:49705400-49715800	Weak transcription	Fetal Intestine Large	intestine
28	chr5:49705600-49709800	Weak transcription	Primary neutrophils fromperipheralblood	blood
29	chr5:49706000-49708000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr5:49706000-49708200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr5:49706200-49709800	Weak transcription	Primary B cells from cord blood	blood
32	chr5:49706600-49708200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
33	chr5:49706800-49710000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
34	chr5:49707000-49708800	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr5:49707200-49708200	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr5:49707200-49708400	Enhancers	iPS-20b Cell Line	embryonic stem cell
37	chr5:49707200-49715000	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr5:49707600-49708000	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr5:49707600-49708600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
40	chr5:49707600-49708800	Weak transcription	Primary T helper cells fromperipheralblood	blood
41	chr5:49707600-49709000	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr5:49707600-49709800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

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