Variant report

Variant	rs55901988
Chromosome Location	chr12:51704572-51704573
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:51702787..51706135-chr12:51715860..51718375,3	K562	blood:
2	chr12:51701016..51703258-chr12:51704233..51707521,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000110934	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs12578771	0.93[EUR][1000 genomes]
rs12580302	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12581282	0.93[EUR][1000 genomes]
rs17860277	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860287	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860296	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860302	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17860346	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860364	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860365	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860378	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860380	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860382	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17860387	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1991433	0.82[EUR][1000 genomes]
rs2288367	0.86[EUR][1000 genomes]
rs3858637	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs57484374	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58213562	0.93[EUR][1000 genomes]
rs58673573	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs60641385	0.93[EUR][1000 genomes]
rs60797544	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs61172662	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61380773	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61570206	0.93[EUR][1000 genomes]
rs61605107	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7138394	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7308177	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7311196	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7312857	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7316221	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7316301	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7316604	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74093810	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74093814	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs74093823	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74093827	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs74093853	0.89[EUR][1000 genomes]
rs7975715	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv482304	chr12:51653496-51814917	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv469377	chr12:51690751-51733951	Enhancers Active TSS Flanking Active TSS Weak transcription Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv558877	chr12:51690751-51733951	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv832408	chr12:51696605-51871339	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51681800-51714200	Weak transcription	Gastric	stomach
2	chr12:51687000-51707400	Strong transcription	Primary monocytes fromperipheralblood	blood
3	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
4	chr12:51696600-51712400	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr12:51698400-51712600	Weak transcription	Spleen	Spleen
6	chr12:51699200-51709400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
7	chr12:51699800-51710000	Strong transcription	Fetal Thymus	thymus
8	chr12:51700600-51711000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr12:51701400-51704800	Strong transcription	Primary B cells from peripheral blood	blood
10	chr12:51701400-51706800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
11	chr12:51701400-51708600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
12	chr12:51701600-51706400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
13	chr12:51701600-51706600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
14	chr12:51701600-51708400	Genic enhancers	Primary T helper cells fromperipheralblood	blood
15	chr12:51702000-51705400	Strong transcription	Primary hematopoietic stem cells	blood
16	chr12:51702200-51712400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:51702400-51705800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
18	chr12:51702400-51705800	Weak transcription	Pancreas	Pancrea
19	chr12:51702400-51709600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr12:51702400-51712200	Weak transcription	GM12878-XiMat	blood
21	chr12:51702600-51705600	Weak transcription	NHEK	skin
22	chr12:51702600-51709000	Weak transcription	K562	blood
23	chr12:51702800-51705000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr12:51702800-51712200	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr12:51703000-51704600	Strong transcription	Primary B cells from cord blood	blood
26	chr12:51703200-51705400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:51703200-51707400	Weak transcription	Duodenum Mucosa	Duodenum
28	chr12:51703200-51709800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr12:51703400-51711200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr12:51703400-51711200	Weak transcription	Placenta	Placenta
31	chr12:51703600-51704600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr12:51703800-51705000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
33	chr12:51704000-51704800	Genic enhancers	Primary T cells from cord blood	blood
34	chr12:51704000-51705600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:51704000-51712200	Weak transcription	Stomach Mucosa	stomach
36	chr12:51704200-51704800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
37	chr12:51704200-51705000	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr12:51704200-51706000	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr12:51704400-51712200	Weak transcription	A549	lung

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