Variant report

Variant	rs609885
Chromosome Location	chr11:86378610-86378611
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:86377391..86379376-chr11:86389767..86391920,2	MCF-7	breast:
2	chr11:86377275..86378822-chr11:86510108..86512716,2	MCF-7	breast:
3	chr11:86377242..86379292-chr11:86431051..86433926,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000150687	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10792865	0.90[CHB][hapmap]
rs10792872	0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2508305	0.85[CHB][hapmap]
rs4319536	0.90[CHB][hapmap]
rs4592448	0.90[CHB][hapmap]
rs493010	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs503155	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs507211	0.83[AMR][1000 genomes]
rs538058	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.88[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs539805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs589887	0.99[ASN][1000 genomes]
rs591060	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs597823	0.88[ASN][1000 genomes]
rs622933	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs624183	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs627684	0.86[YRI][hapmap]
rs648258	0.90[ASN][1000 genomes]
rs661954	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs668753	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs674053	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs679220	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs688119	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs693817	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9735826	0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044081	chr11:86133641-86868560	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv541118	chr11:86133641-86868560	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
3	nsv555665	chr11:86230898-86417553	Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055071	chr11:86301240-86465465	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv555704	chr11:86344677-86386784	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv428263	chr11:86357990-86508480	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:86366200-86380000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr11:86366600-86379800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr11:86369800-86379600	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:86369800-86379600	Weak transcription	Lung	lung
5	chr11:86369800-86379800	Weak transcription	Brain Anterior Caudate	brain
6	chr11:86369800-86381200	Weak transcription	Pancreas	Pancrea
7	chr11:86369800-86382000	Weak transcription	Fetal Muscle Leg	muscle
8	chr11:86370000-86382000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr11:86370400-86379600	Weak transcription	Fetal Brain Female	brain
10	chr11:86370600-86379400	Weak transcription	Fetal Brain Male	brain
11	chr11:86371200-86380800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr11:86371400-86379600	Weak transcription	Right Atrium	heart
13	chr11:86371400-86381000	Weak transcription	HUVEC	blood vessel
14	chr11:86371400-86381000	Weak transcription	NHLF	lung
15	chr11:86371400-86381200	Weak transcription	Stomach Mucosa	stomach
16	chr11:86371400-86381400	Weak transcription	HSMM	muscle
17	chr11:86371600-86380800	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:86372400-86381200	Weak transcription	NHDF-Ad	bronchial
19	chr11:86372800-86379600	Weak transcription	Brain Angular Gyrus	brain
20	chr11:86373000-86381200	Weak transcription	Primary T cells from cord blood	blood
21	chr11:86373000-86381200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:86373600-86382000	Weak transcription	Fetal Muscle Trunk	muscle
23	chr11:86374600-86380200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr11:86374600-86380200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr11:86374600-86381200	Weak transcription	Brain Cingulate Gyrus	brain
26	chr11:86374600-86381200	Weak transcription	Brain Hippocampus Middle	brain
27	chr11:86374800-86381000	Weak transcription	Adipose Nuclei	Adipose
28	chr11:86374800-86381200	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr11:86375800-86379600	Weak transcription	Brain Germinal Matrix	brain
30	chr11:86375800-86380200	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr11:86375800-86380200	Weak transcription	Rectal Smooth Muscle	rectum
32	chr11:86375800-86382000	Weak transcription	Fetal Intestine Small	intestine
33	chr11:86376000-86380000	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:86376000-86381400	Weak transcription	Small Intestine	intestine
35	chr11:86376000-86382000	Weak transcription	Fetal Intestine Large	intestine
36	chr11:86376200-86379800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr11:86376200-86380000	Weak transcription	Ovary	ovary
38	chr11:86376200-86382400	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr11:86376400-86380000	Weak transcription	Stomach Smooth Muscle	stomach
40	chr11:86376600-86381000	Weak transcription	Fetal Stomach	stomach
41	chr11:86377600-86379600	Weak transcription	Skeletal Muscle Female	skeletal muscle
42	chr11:86377600-86380200	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr11:86377600-86380400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr11:86377600-86381000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr11:86377600-86381000	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr11:86377800-86381000	Weak transcription	Fetal Kidney	kidney
47	chr11:86377800-86381200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr11:86377800-86381200	Weak transcription	Colonic Mucosa	Colon
49	chr11:86377800-86381600	Weak transcription	NHEK	skin
50	chr11:86377800-86382000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links