Variant report

Variant	rs4756288
Chromosome Location	chr11:36178765-36178766
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36177041..36178787-chr11:36285024..36287447,2	MCF-7	breast:

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs10836512	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11033468	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1105373	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204508	1.00[JPT][hapmap]
rs4450151	1.00[JPT][hapmap]
rs4756289	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4756295	1.00[JPT][hapmap]
rs57412870	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6484826	1.00[JPT][hapmap]
rs6484828	1.00[JPT][hapmap]
rs7110901	1.00[JPT][hapmap]
rs7111128	1.00[JPT][hapmap]
rs7111826	0.80[YRI][hapmap]
rs7481996	1.00[JPT][hapmap]
rs7931368	1.00[JPT][hapmap]

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	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv897225	chr11:36136912-36244190	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4756288	SLC1A2	cis	parietal	SCAN
rs4756288	TCP11L1	cis	parietal	SCAN

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36171400-36184000	Weak transcription	Right Atrium	heart
2	chr11:36171600-36187800	Weak transcription	Spleen	Spleen
3	chr11:36172000-36184000	Weak transcription	Pancreas	Pancrea
4	chr11:36172000-36184200	Weak transcription	Fetal Intestine Small	intestine
5	chr11:36172600-36183400	Weak transcription	Hela-S3	cervix
6	chr11:36172600-36190400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr11:36173000-36183200	Weak transcription	HSMMtube	muscle
8	chr11:36173600-36179600	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr11:36174600-36179600	Enhancers	Ovary	ovary
10	chr11:36175000-36180000	Enhancers	Fetal Lung	lung
11	chr11:36175000-36184000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr11:36175200-36179600	Enhancers	Fetal Stomach	stomach
13	chr11:36175200-36183800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr11:36175400-36181400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr11:36175600-36184000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
16	chr11:36175600-36184200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr11:36175800-36179200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr11:36175800-36179800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr11:36175800-36180000	Enhancers	Fetal Muscle Leg	muscle
20	chr11:36176000-36179800	Enhancers	HUVEC	blood vessel
21	chr11:36176200-36179400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr11:36176400-36179000	Enhancers	Fetal Brain Female	brain
23	chr11:36176400-36179200	Enhancers	NHLF	lung
24	chr11:36176400-36179400	Enhancers	NHDF-Ad	bronchial
25	chr11:36176600-36179200	Enhancers	Brain Cingulate Gyrus	brain
26	chr11:36176600-36184000	Weak transcription	Right Ventricle	heart
27	chr11:36176800-36181400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr11:36176800-36181400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr11:36177200-36178800	Enhancers	Stomach Smooth Muscle	stomach
30	chr11:36177200-36179400	Enhancers	Muscle Satellite Cultured Cells	--
31	chr11:36177200-36179400	Enhancers	HSMM	muscle
32	chr11:36177200-36179600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr11:36177400-36179000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr11:36177400-36179000	Enhancers	HMEC	breast
35	chr11:36177400-36179600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr11:36177600-36178800	Flanking Active TSS	Brain Germinal Matrix	brain
37	chr11:36177800-36178800	Weak transcription	H1 Cell Line	embryonic stem cell
38	chr11:36177800-36178800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
39	chr11:36177800-36179000	Enhancers	Adipose Nuclei	Adipose
40	chr11:36177800-36179600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr11:36177800-36179600	Enhancers	Osteobl	bone
42	chr11:36177800-36181200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr11:36178000-36179200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr11:36178000-36181400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
45	chr11:36178000-36184000	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr11:36178200-36178800	Enhancers	Fetal Heart	heart
47	chr11:36178200-36179200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr11:36178200-36179200	Enhancers	NHEK	skin
49	chr11:36178200-36181400	Weak transcription	Lung	lung
50	chr11:36178200-36183200	Weak transcription	Rectal Smooth Muscle	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links