Variant report

Variant	rs578452
Chromosome Location	chr6:33581011-33581012
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	chr6:33576666..33582891-chr6:33586745..33591603,10	MCF-7	breast:
2	chr6:33574216..33577618-chr6:33579266..33582393,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000096433	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10947416	0.94[AFR][1000 genomes]
rs1536043	0.94[AFR][1000 genomes]
rs16869280	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1794681	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1794682	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2894349	0.89[ASN][1000 genomes]
rs4711332	0.82[AFR][1000 genomes]
rs4713641	0.94[AFR][1000 genomes]
rs4713642	0.94[AFR][1000 genomes]
rs4713643	0.82[AFR][1000 genomes]
rs475982	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs494654	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs499384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7750812	0.91[AFR][1000 genomes]
rs7753712	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7753829	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7768401	0.91[AFR][1000 genomes]
rs7769019	0.91[AFR][1000 genomes]
rs7772766	0.82[AFR][1000 genomes]
rs7775537	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9348920	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9394157	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9469529	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv462896	chr6:33534880-33588147	Bivalent Enhancer Flanking Active TSS Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv602833	chr6:33534880-33588147	Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv885770	chr6:33543409-33614127	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
4	nsv830638	chr6:33551202-33711346	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	46 gene(s)	inside rSNPs	diseases
5	nsv5250	chr6:33565017-33598370	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:33574400-33583200	Enhancers	HMEC	breast
2	chr6:33574600-33582400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:33577400-33583000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr6:33578000-33587000	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr6:33578400-33581200	Weak transcription	HUVEC	blood vessel
6	chr6:33578800-33588000	Weak transcription	Gastric	stomach
7	chr6:33579000-33581200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr6:33579000-33581400	Weak transcription	Placenta	Placenta
9	chr6:33579000-33583800	Weak transcription	Right Ventricle	heart
10	chr6:33579200-33581400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr6:33579200-33581400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr6:33579200-33586600	Weak transcription	Fetal Lung	lung
13	chr6:33579200-33587000	Weak transcription	Pancreas	Pancrea
14	chr6:33579400-33581200	Weak transcription	Brain Cingulate Gyrus	brain
15	chr6:33579400-33581600	Weak transcription	Spleen	Spleen
16	chr6:33579400-33587000	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr6:33579400-33587000	Weak transcription	Right Atrium	heart
18	chr6:33579400-33588000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr6:33579600-33581200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr6:33579600-33581200	Weak transcription	H1 Cell Line	embryonic stem cell
21	chr6:33580000-33581200	Enhancers	Hela-S3	cervix
22	chr6:33580000-33581600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr6:33580000-33581600	Weak transcription	Colonic Mucosa	Colon
24	chr6:33580000-33581600	Weak transcription	Left Ventricle	heart
25	chr6:33580000-33586800	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr6:33580000-33587600	Weak transcription	Brain Substantia Nigra	brain
27	chr6:33580200-33581400	Weak transcription	A549	lung
28	chr6:33580800-33581200	Enhancers	Muscle Satellite Cultured Cells	--
29	chr6:33580800-33581800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr6:33580800-33582400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr6:33580800-33582400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr6:33580800-33583000	Enhancers	NHDF-Ad	bronchial
33	chr6:33580800-33583400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr6:33581000-33581200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr6:33581000-33581200	Flanking Active TSS	HSMM	muscle
36	chr6:33581000-33581400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr6:33581000-33581400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr6:33581000-33581400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr6:33581000-33581400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:33581000-33581400	Enhancers	Brain Inferior Temporal Lobe	brain
41	chr6:33581000-33581600	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr6:33581000-33581600	Enhancers	Brain Anterior Caudate	brain
43	chr6:33581000-33581600	Enhancers	Brain Hippocampus Middle	brain
44	chr6:33581000-33582000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:33581000-33582000	Enhancers	Esophagus	oesophagus
46	chr6:33581000-33582000	Enhancers	Fetal Intestine Small	intestine
47	chr6:33581000-33582000	Enhancers	Placenta Amnion	Placenta Amnion
48	chr6:33581000-33582000	Flanking Active TSS	HepG2	liver
49	chr6:33581000-33582000	Enhancers	NHLF	lung
50	chr6:33581000-33582000	Flanking Active TSS	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links