Variant report

Variant	rs7725954
Chromosome Location	chr5:49708458-49708459
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs10044854	1.00[EUR][1000 genomes]
rs10052275	1.00[EUR][1000 genomes]
rs10052791	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10057052	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs10060305	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10060422	1.00[EUR][1000 genomes]
rs10061275	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10061475	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10071541	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10075105	1.00[EUR][1000 genomes]
rs10077753	1.00[EUR][1000 genomes]
rs10155555	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10471741	1.00[EUR][1000 genomes]
rs11956767	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13361719	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13362259	1.00[EUR][1000 genomes]
rs16879103	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16879123	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1839128	1.00[CHB][hapmap]
rs303224	0.81[ASN][1000 genomes]
rs59712310	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59909598	1.00[EUR][1000 genomes]
rs59960546	1.00[EUR][1000 genomes]
rs60272168	1.00[EUR][1000 genomes]
rs60549055	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60805453	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61193294	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61628676	1.00[EUR][1000 genomes]
rs6863584	1.00[EUR][1000 genomes]
rs6876049	1.00[EUR][1000 genomes]
rs6880021	1.00[EUR][1000 genomes]
rs72751717	0.91[ASN][1000 genomes]
rs73100073	1.00[EUR][1000 genomes]
rs73104231	1.00[ASN][1000 genomes]
rs73104234	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73104242	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73104251	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7702350	0.97[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7704643	1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7722908	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723096	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7723166	1.00[EUR][1000 genomes];0.87[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	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

No data

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	chr5:49697000-49723400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr5:49697400-49723400	Weak transcription	HSMM	muscle
7	chr5:49697600-49709800	Weak transcription	Primary T cells from cord blood	blood
8	chr5:49697600-49719000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr5:49697600-49721600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr5:49698200-49711600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr5:49701000-49711400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr5:49703200-49709200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr5:49703200-49719000	Weak transcription	HMEC	breast
14	chr5:49703200-49724600	Weak transcription	Primary hematopoietic stem cells	blood
15	chr5:49703200-49727000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr5:49703400-49711800	Weak transcription	Primary monocytes fromperipheralblood	blood
17	chr5:49703600-49711400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr5:49704200-49710000	Weak transcription	Fetal Intestine Small	intestine
19	chr5:49704400-49711600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr5:49705200-49709200	Enhancers	Primary T helper naive cells from peripheral blood	blood
21	chr5:49705200-49710600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr5:49705400-49709400	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr5:49705400-49715800	Weak transcription	Fetal Intestine Large	intestine
24	chr5:49705600-49709800	Weak transcription	Primary neutrophils fromperipheralblood	blood
25	chr5:49706200-49709800	Weak transcription	Primary B cells from cord blood	blood
26	chr5:49706800-49710000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr5:49707000-49708800	Enhancers	iPS-18 Cell Line	embryonic stem cell
28	chr5:49707200-49715000	Enhancers	Primary T helper cells PMA-I stimulated	--
29	chr5:49707600-49708600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr5:49707600-49708800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr5:49707600-49709000	Enhancers	HUES48 Cell Line	embryonic stem cell
32	chr5:49707600-49709800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
33	chr5:49708000-49708600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
34	chr5:49708000-49708600	Enhancers	Primary T killer memory cells from peripheral blood	blood
35	chr5:49708000-49709000	Enhancers	HUES64 Cell Line	embryonic stem cell
36	chr5:49708000-49709000	Enhancers	iPS-15b Cell Line	embryonic stem cell
37	chr5:49708200-49708600	Enhancers	ES-I3 Cell Line	embryonic stem cell
38	chr5:49708200-49708600	Enhancers	HUES6 Cell Line	embryonic stem cell
39	chr5:49708200-49708600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr5:49708200-49708800	Enhancers	Primary B cells from peripheral blood	blood
41	chr5:49708200-49710000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr5:49708400-49708800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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