Variant report

Variant	rs12576997
Chromosome Location	chr11:9709778-9709779
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9708443..9711288-chr11:9711524..9713112,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs11042471	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042472	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042473	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042474	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042475	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042477	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11042478	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12272167	0.82[AMR][1000 genomes]
rs12275468	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12291809	0.88[ASN][1000 genomes]
rs12295129	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12577241	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1390680	0.82[AMR][1000 genomes]
rs1496477	0.82[AMR][1000 genomes]
rs2088293	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2101902	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572936	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572937	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572938	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572941	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2572947	0.83[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2572948	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572949	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2572952	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2645014	0.83[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs2645015	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2645018	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645019	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645021	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645022	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645023	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2645024	0.82[AMR][1000 genomes]
rs2649047	0.82[AMR][1000 genomes]
rs34780673	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs360044	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360045	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360046	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs360048	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs360050	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs360052	0.96[ASN][1000 genomes]
rs360053	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs416766	0.82[AMR][1000 genomes]
rs57239484	0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs67598578	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73408298	0.84[EUR][1000 genomes]
rs73408300	0.88[EUR][1000 genomes]
rs73410140	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs920081	0.82[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv933855	chr11:9645441-10130519	Strong transcription Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv1053369	chr11:9647837-9876054	Genic enhancers Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv553468	chr11:9667828-9827871	Weak transcription Genic enhancers Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9686600-9711200	Weak transcription	Esophagus	oesophagus
2	chr11:9686800-9710800	Weak transcription	Aorta	Aorta
3	chr11:9686800-9716400	Weak transcription	Ovary	ovary
4	chr11:9687200-9710200	Weak transcription	Hela-S3	cervix
5	chr11:9687400-9710800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr11:9688200-9710000	Weak transcription	A549	lung
7	chr11:9693200-9710000	Weak transcription	Fetal Thymus	thymus
8	chr11:9695200-9709800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr11:9697000-9709800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr11:9697800-9709800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr11:9700600-9710000	Weak transcription	Monocytes-CD14+_RO01746	blood
12	chr11:9701000-9712800	Weak transcription	Small Intestine	intestine
13	chr11:9702800-9709800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr11:9702800-9709800	Weak transcription	Duodenum Mucosa	Duodenum
15	chr11:9702800-9711000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr11:9702800-9711200	Weak transcription	Lung	lung
17	chr11:9703200-9710800	Weak transcription	Fetal Muscle Leg	muscle
18	chr11:9703400-9710800	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr11:9703600-9709800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:9703600-9711000	Weak transcription	Fetal Intestine Large	intestine
21	chr11:9703800-9709800	Weak transcription	Primary monocytes fromperipheralblood	blood
22	chr11:9703800-9709800	Weak transcription	Gastric	stomach
23	chr11:9703800-9709800	Weak transcription	Right Atrium	heart
24	chr11:9703800-9710000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr11:9703800-9710000	Weak transcription	Spleen	Spleen
26	chr11:9703800-9710200	Weak transcription	Duodenum Smooth Muscle	Duodenum
27	chr11:9703800-9710800	Genic enhancers	Primary B cells from peripheral blood	blood
28	chr11:9703800-9714400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr11:9704200-9723600	Weak transcription	HepG2	liver
30	chr11:9704600-9709800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr11:9705000-9709800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr11:9705000-9711200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
33	chr11:9705200-9710600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr11:9705400-9709800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr11:9705400-9709800	Weak transcription	HUES48 Cell Line	embryonic stem cell
36	chr11:9705400-9709800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr11:9705400-9709800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr11:9705400-9710000	Weak transcription	H1 Cell Line	embryonic stem cell
39	chr11:9705400-9710000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
40	chr11:9705600-9711200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr11:9705800-9709800	Weak transcription	Left Ventricle	heart
42	chr11:9706000-9709800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr11:9706000-9709800	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr11:9706800-9710200	Weak transcription	Fetal Intestine Small	intestine
45	chr11:9707400-9710000	Genic enhancers	Primary B cells from cord blood	blood
46	chr11:9707600-9709800	Weak transcription	Primary T cells from cord blood	blood
47	chr11:9708200-9711200	Weak transcription	Pancreas	Pancrea
48	chr11:9708400-9711800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr11:9708400-9712000	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr11:9708600-9709800	Weak transcription	HSMM	muscle

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