Variant report

Variant	rs11898394
Chromosome Location	chr2:98589654-98589655
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:98586492..98590623-chr2:98609849..98613256,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000075568	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs11892146	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11895466	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900781	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs11900903	1.00[AMR][1000 genomes]
rs1503201	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1503203	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022209	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022289	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022557	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17022726	1.00[AMR][1000 genomes]
rs17022736	1.00[AMR][1000 genomes]
rs17025339	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs35774346	0.82[AFR][1000 genomes]
rs56065241	1.00[AMR][1000 genomes]
rs57434542	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58187838	1.00[AMR][1000 genomes]
rs60828800	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60885334	1.00[AMR][1000 genomes]
rs61712471	1.00[AMR][1000 genomes]
rs6543226	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6726775	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6734701	1.00[AMR][1000 genomes]
rs6736475	1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6737992	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6742955	1.00[YRI][hapmap]
rs6746457	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942824	1.00[AMR][1000 genomes]
rs72942830	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942834	1.00[AMR][1000 genomes]
rs72942836	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942856	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942862	1.00[AMR][1000 genomes]
rs72942871	1.00[AMR][1000 genomes]
rs72942872	1.00[AMR][1000 genomes]
rs72942876	1.00[AMR][1000 genomes]
rs72942885	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942896	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72942898	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944808	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944812	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944813	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944818	0.90[AFR][1000 genomes]
rs72944825	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944834	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72944842	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946409	1.00[AMR][1000 genomes]
rs72946417	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946421	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946425	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946431	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946447	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72946448	1.00[AMR][1000 genomes]
rs72946453	1.00[AMR][1000 genomes]
rs7579764	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9308889	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526360	chr2:98403683-98814054	Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv521568	chr2:98403683-98826203	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	nsv1004220	chr2:98423421-98816010	Weak transcription Enhancers Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1007259	chr2:98429744-98818080	Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv535832	chr2:98429744-98818080	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv1009218	chr2:98442640-98816010	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
7	nsv1003925	chr2:98442640-98821102	Enhancers Strong transcription Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv999442	chr2:98448732-98816010	Weak transcription Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv1013902	chr2:98454309-98818080	ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv1013416	chr2:98472701-98688729	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats 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	7 gene(s)	inside rSNPs	diseases
11	nsv518056	chr2:98586842-99156296	Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
12	esv3451267	chr2:98588690-98590336	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:98568200-98599200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr2:98568400-98592000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:98575200-98592600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr2:98575400-98595000	Weak transcription	HSMM	muscle
5	chr2:98580000-98589800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr2:98583600-98595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr2:98584600-98590000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:98584600-98597000	Weak transcription	Thymus	Thymus
9	chr2:98585000-98608400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:98585200-98589800	Weak transcription	Primary B cells from cord blood	blood
11	chr2:98585400-98591200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr2:98585600-98594800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr2:98586800-98590600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr2:98587000-98594800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:98587000-98595600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr2:98587200-98589800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr2:98587200-98589800	Weak transcription	Right Atrium	heart
18	chr2:98587200-98590000	Weak transcription	Primary T cells from cord blood	blood
19	chr2:98587200-98591200	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr2:98587400-98589800	Weak transcription	Left Ventricle	heart
21	chr2:98587400-98592400	Weak transcription	Ovary	ovary
22	chr2:98587400-98599600	Weak transcription	Spleen	Spleen
23	chr2:98587800-98595400	Weak transcription	Primary T helper cells fromperipheralblood	blood
24	chr2:98587800-98600000	Weak transcription	Gastric	stomach
25	chr2:98588200-98592600	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
26	chr2:98588200-98596000	Weak transcription	Stomach Mucosa	stomach
27	chr2:98588400-98590200	Enhancers	Psoas Muscle	Psoas
28	chr2:98588600-98590400	Weak transcription	Pancreas	Pancrea
29	chr2:98588600-98598200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
30	chr2:98589000-98590200	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr2:98589000-98590400	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr2:98589000-98590600	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
33	chr2:98589200-98590000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr2:98589200-98590000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr2:98589200-98590200	ZNF genes & repeats	GM12878-XiMat	blood
36	chr2:98589200-98591600	ZNF genes & repeats	Primary B cells from peripheral blood	blood
37	chr2:98589200-98597400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr2:98589400-98590000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr2:98589400-98592000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr2:98589600-98590000	ZNF genes & repeats	Fetal Lung	lung
41	chr2:98589600-98590200	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr2:98589600-98591000	ZNF genes & repeats	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links