Variant report

Variant	rs11609872
Chromosome Location	chr12:116975386-116975387
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:116870032..116871655-chr12:116975308..116976857,2	MCF-7	breast:
2	chr12:116957046..116958722-chr12:116975166..116976797,2	MCF-7	breast:
3	chr12:116971915..116975712-chr12:116994698..116997472,3	MCF-7	breast:
4	chr12:116970629..116972206-chr12:116974747..116977388,2	MCF-7	breast:
5	chr12:116827977..116830260-chr12:116974076..116977049,2	MCF-7	breast:
6	chr12:116974299..116976845-chr12:116980092..116981659,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171471	Chromatin interaction
ENSG00000196668	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10774871	0.87[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs10774872	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs10850662	0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs10850663	0.87[ASN][1000 genomes]
rs11068062	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs11068070	0.82[ASN][1000 genomes]
rs11068075	0.84[ASN][1000 genomes]
rs11609040	0.87[ASN][1000 genomes]
rs11610226	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11615960	0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1394801	0.94[ASN][1000 genomes]
rs1394802	0.93[CHB][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs2047952	0.82[ASN][1000 genomes]
rs2089222	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2102294	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs2893685	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60521218	0.87[ASN][1000 genomes]
rs6490075	0.86[ASN][1000 genomes]
rs6490076	0.87[CHB][hapmap];0.94[JPT][hapmap];0.82[ASN][1000 genomes]
rs7297552	0.82[ASN][1000 genomes]
rs7300418	0.87[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs7304300	0.82[ASN][1000 genomes]
rs7315385	0.82[ASN][1000 genomes]
rs7954181	0.89[ASN][1000 genomes]
rs7961538	0.87[ASN][1000 genomes]
rs7969190	0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs7969566	0.93[CHB][hapmap];0.94[JPT][hapmap];0.85[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7972701	0.82[ASN][1000 genomes]
rs7976256	0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899540	chr12:116920503-116999861	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:116972200-116975600	Weak transcription	Small Intestine	intestine
2	chr12:116972400-116978400	Enhancers	Primary B cells from peripheral blood	blood
3	chr12:116972600-116976200	Weak transcription	Rectal Mucosa Donor 31	rectum
4	chr12:116972600-116976600	Weak transcription	Right Atrium	heart
5	chr12:116972600-116976800	Weak transcription	Brain Substantia Nigra	brain
6	chr12:116972600-116976800	Weak transcription	HUVEC	blood vessel
7	chr12:116972600-116977400	Weak transcription	HSMM	muscle
8	chr12:116972600-116977600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr12:116972600-116977800	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:116972800-116976200	Weak transcription	Adipose Nuclei	Adipose
11	chr12:116972800-116976400	Weak transcription	Primary hematopoietic stem cells	blood
12	chr12:116972800-116976400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr12:116972800-116976400	Weak transcription	Esophagus	oesophagus
14	chr12:116972800-116976400	Weak transcription	Lung	lung
15	chr12:116972800-116976400	Weak transcription	Pancreas	Pancrea
16	chr12:116972800-116976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr12:116972800-116976400	Weak transcription	HMEC	breast
18	chr12:116972800-116976600	Weak transcription	Left Ventricle	heart
19	chr12:116972800-116976800	Weak transcription	Hela-S3	cervix
20	chr12:116972800-116977000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr12:116972800-116977000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr12:116972800-116977200	Weak transcription	Liver	Liver
23	chr12:116972800-116977200	Weak transcription	Brain Hippocampus Middle	brain
24	chr12:116972800-116977200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr12:116972800-116977200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr12:116972800-116977200	Weak transcription	Fetal Lung	lung
27	chr12:116972800-116977200	Weak transcription	Psoas Muscle	Psoas
28	chr12:116972800-116977600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:116972800-116977600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr12:116972800-116977600	Weak transcription	Right Ventricle	heart
31	chr12:116972800-116977800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr12:116972800-116980400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr12:116972800-116982000	Weak transcription	Ovary	ovary
34	chr12:116973000-116976200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr12:116973000-116976200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
36	chr12:116973000-116976200	Weak transcription	Duodenum Smooth Muscle	Duodenum
37	chr12:116973000-116976200	Weak transcription	Fetal Intestine Large	intestine
38	chr12:116973000-116976200	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr12:116973000-116976200	Weak transcription	Skeletal Muscle Female	skeletal muscle
40	chr12:116973000-116976400	Weak transcription	HUES48 Cell Line	embryonic stem cell
41	chr12:116973000-116976400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
42	chr12:116973000-116976400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr12:116973000-116976600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr12:116973000-116976800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr12:116973000-116977000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr12:116973000-116977000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr12:116973000-116977000	Weak transcription	Skeletal Muscle Male	skeletal muscle
48	chr12:116973000-116977000	Weak transcription	NH-A	brain
49	chr12:116973000-116977200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr12:116973000-116977200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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