Variant report

Variant	rs61882460
Chromosome Location	chr11:18009788-18009789
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:18007709..18010705-chr11:18020081..18022716,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000129158	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs17720417	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17720513	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17721184	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17794213	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs211126	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211127	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs211134	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs211138	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2237912	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2237921	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2237924	0.81[AMR][1000 genomes]
rs2283236	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2283239	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34614478	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs394218	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3993323	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3993324	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs440234	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4438010	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4756927	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4757604	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4757605	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4757606	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61882454	0.81[AMR][1000 genomes]
rs61882456	0.90[AMR][1000 genomes];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61882461	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884488	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884489	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61884492	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884493	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61884494	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs758437	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.96[ASN][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	nsv949248	chr11:17791822-18692687	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	156 gene(s)	inside rSNPs	diseases
2	nsv897026	chr11:17823296-18084878	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv832079	chr11:17927967-18047743	Flanking Active TSS Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:17934400-18033600	Weak transcription	Small Intestine	intestine
2	chr11:17944000-18026600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:17945400-18010000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr11:17945400-18033400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr11:17961000-18016200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr11:17966400-18014400	Weak transcription	Fetal Thymus	thymus
7	chr11:17971200-18026000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:17975000-18020200	Weak transcription	A549	lung
9	chr11:17978200-18016200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr11:17979800-18016400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr11:17980400-18033600	Weak transcription	Colonic Mucosa	Colon
12	chr11:17981200-18033200	Weak transcription	Esophagus	oesophagus
13	chr11:17989400-18023400	Weak transcription	Gastric	stomach
14	chr11:17989400-18033400	Weak transcription	Pancreas	Pancrea
15	chr11:17991000-18027000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr11:17994000-18033400	Weak transcription	Pancreatic Islets	Pancreatic Islet
17	chr11:17994600-18012200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr11:17996600-18032400	Weak transcription	Fetal Brain Male	brain
19	chr11:17998200-18012200	Strong transcription	Primary T cells from cord blood	blood
20	chr11:17998400-18033200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr11:17999000-18009800	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr11:17999000-18009800	Weak transcription	Thymus	Thymus
23	chr11:18000800-18014600	Weak transcription	Spleen	Spleen
24	chr11:18002400-18033800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr11:18002600-18010600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
26	chr11:18002600-18012200	Strong transcription	Primary T helper cells fromperipheralblood	blood
27	chr11:18002800-18012200	Strong transcription	Primary B cells from peripheral blood	blood
28	chr11:18003600-18012400	Strong transcription	Primary T cells fromperipheralblood	blood
29	chr11:18003800-18011400	Strong transcription	Monocytes-CD14+_RO01746	blood
30	chr11:18004000-18011000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:18005000-18010400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
32	chr11:18005200-18010200	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr11:18005200-18010200	Strong transcription	Brain Anterior Caudate	brain
34	chr11:18005200-18010400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:18005400-18010400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr11:18005400-18011000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
37	chr11:18005600-18010200	Strong transcription	Adipose Nuclei	Adipose
38	chr11:18005600-18011400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr11:18005600-18012000	Strong transcription	Duodenum Mucosa	Duodenum
40	chr11:18005800-18010200	Strong transcription	Brain Germinal Matrix	brain
41	chr11:18005800-18010400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr11:18005800-18011200	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr11:18006200-18010400	Strong transcription	Primary T helper cells PMA-I stimulated	--
44	chr11:18006400-18010400	Strong transcription	GM12878-XiMat	blood
45	chr11:18006800-18010200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr11:18006800-18010400	Strong transcription	Primary monocytes fromperipheralblood	blood
47	chr11:18006800-18010400	Strong transcription	Fetal Muscle Trunk	muscle
48	chr11:18006800-18021000	Weak transcription	Placenta	Placenta
49	chr11:18007000-18010000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
50	chr11:18007000-18012200	Strong transcription	Rectal Mucosa Donor 31	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links