Variant report

Variant	rs11169800
Chromosome Location	chr12:51701769-51701770
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:51701016..51703258-chr12:51704233..51707521,3	MCF-7	breast:
2	chr12:51694624..51697203-chr12:51700162..51702400,2	MCF-7	breast:
3	chr12:51696998..51699958-chr12:51701711..51703812,2	K562	blood:
4	chr12:51661276..51664134-chr12:51700484..51702022,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170545	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12580302	0.80[ASN][1000 genomes]
rs12580599	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814917	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4335588	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56869579	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs57484374	0.83[ASN][1000 genomes]
rs61172662	0.84[ASN][1000 genomes]
rs7301933	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7309232	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs74093823	0.84[ASN][1000 genomes]
rs74093827	0.84[ASN][1000 genomes]
rs7975534	0.83[EUR][1000 genomes]
rs9652000	0.85[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:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:51674200-51704000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr12:51681800-51714200	Weak transcription	Gastric	stomach
3	chr12:51686200-51702800	Weak transcription	Colonic Mucosa	Colon
4	chr12:51687000-51703800	Strong transcription	Primary neutrophils fromperipheralblood	blood
5	chr12:51687000-51707400	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr12:51687800-51708000	Strong transcription	Thymus	Thymus
7	chr12:51691800-51702200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:51696600-51712400	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr12:51698200-51702200	Weak transcription	Placenta	Placenta
10	chr12:51698400-51712600	Weak transcription	Spleen	Spleen
11	chr12:51699200-51709400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
12	chr12:51699800-51710000	Strong transcription	Fetal Thymus	thymus
13	chr12:51700000-51701800	Strong transcription	Primary T cells from cord blood	blood
14	chr12:51700000-51702400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr12:51700200-51702000	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
16	chr12:51700400-51701800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:51700600-51703000	Weak transcription	Esophagus	oesophagus
18	chr12:51700600-51711000	Strong transcription	Monocytes-CD14+_RO01746	blood
19	chr12:51700800-51702000	Weak transcription	Primary hematopoietic stem cells	blood
20	chr12:51700800-51703000	Weak transcription	Primary B cells from cord blood	blood
21	chr12:51701200-51702200	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr12:51701200-51704000	Enhancers	Stomach Mucosa	stomach
23	chr12:51701400-51701800	Enhancers	Muscle Satellite Cultured Cells	--
24	chr12:51701400-51702400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
25	chr12:51701400-51702400	Enhancers	NHLF	lung
26	chr12:51701400-51703000	Enhancers	Fetal Intestine Small	intestine
27	chr12:51701400-51703000	Flanking Active TSS	A549	lung
28	chr12:51701400-51703000	Enhancers	Osteobl	bone
29	chr12:51701400-51704000	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
30	chr12:51701400-51704800	Strong transcription	Primary B cells from peripheral blood	blood
31	chr12:51701400-51706800	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr12:51701400-51708600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
33	chr12:51701600-51701800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr12:51701600-51701800	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr12:51701600-51701800	Enhancers	NH-A	brain
36	chr12:51701600-51702000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr12:51701600-51702000	Enhancers	Small Intestine	intestine
38	chr12:51701600-51702200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr12:51701600-51702200	Enhancers	Duodenum Mucosa	Duodenum
40	chr12:51701600-51702200	Enhancers	Sigmoid Colon	Sigmoid Colon
41	chr12:51701600-51702200	Enhancers	HSMM	muscle
42	chr12:51701600-51702400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr12:51701600-51702400	Genic enhancers	Primary T killer naive cells fromperipheralblood	blood
44	chr12:51701600-51702400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:51701600-51702400	Strong transcription	GM12878-XiMat	blood
46	chr12:51701600-51702600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr12:51701600-51702600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr12:51701600-51702600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr12:51701600-51702600	Enhancers	K562	blood
50	chr12:51701600-51702600	Enhancers	NHEK	skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links