Variant report

Variant	rs4619669
Chromosome Location	chr20:52414820-52414821
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:47254709..47255463-chr20:52414569..52415348,2	MCF-7	breast:
2	chr17:56708001..56710383-chr20:52413455..52415056,2	MCF-7	breast:
3	chr20:52406598..52408941-chr20:52412585..52415507,2	K562	blood:
4	chr20:52414372..52415082-chr20:52424509..52425462,2	MCF-7	breast:
5	chr17:57914792..57918180-chr20:52413541..52418064,4	MCF-7	breast:
6	chr17:56707901..56710252-chr20:52413457..52417061,3	MCF-7	breast:
7	chr11:122931494..122933593-chr20:52412455..52415144,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000212195	Chromatin interaction
ENSG00000109971	Chromatin interaction
ENSG00000062716	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1117558	0.95[ASN][1000 genomes]
rs1117559	0.96[ASN][1000 genomes]
rs12625415	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3764716	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4330164	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4361184	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416274	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4416275	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618108	0.99[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56808127	0.94[ASN][1000 genomes]
rs58281268	0.92[ASN][1000 genomes]
rs6123316	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126958	0.94[ASN][1000 genomes]
rs6126962	0.89[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs6126963	0.96[AFR][1000 genomes];0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126964	0.90[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6126969	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126970	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126971	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6126972	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6126973	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62208437	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs67468076	0.96[AFR][1000 genomes];0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34060	chr20:52251863-52702186	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	296 gene(s)	inside rSNPs	diseases
2	nsv834008	chr20:52368660-52533410	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	185 gene(s)	inside rSNPs	diseases
3	nsv834009	chr20:52386050-52590795	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	182 gene(s)	inside rSNPs	diseases
4	nsv1057509	chr20:52390002-52431309	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	64 gene(s)	inside rSNPs	diseases
5	nsv586221	chr20:52392390-52418987	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
6	nsv1064299	chr20:52395560-52420612	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
7	nsv1063442	chr20:52400519-52428220	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
8	nsv1060372	chr20:52409008-52502100	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	122 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52404200-52415600	Weak transcription	Fetal Intestine Large	intestine
2	chr20:52406600-52417200	Weak transcription	K562	blood
3	chr20:52410600-52416400	Weak transcription	Liver	Liver
4	chr20:52411000-52415600	Weak transcription	Pancreas	Pancrea
5	chr20:52411600-52415600	Weak transcription	Esophagus	oesophagus
6	chr20:52411600-52415600	Weak transcription	NHEK	skin
7	chr20:52411800-52415600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr20:52411800-52421400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr20:52412000-52415400	Weak transcription	HMEC	breast
10	chr20:52412000-52417400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr20:52412200-52421600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr20:52412600-52415400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr20:52413600-52416400	Enhancers	HepG2	liver
14	chr20:52413800-52415800	Weak transcription	Colonic Mucosa	Colon
15	chr20:52414000-52415200	Weak transcription	A549	lung
16	chr20:52414000-52421800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr20:52414400-52417200	Enhancers	Rectal Mucosa Donor 31	rectum
18	chr20:52414600-52417000	Enhancers	Rectal Mucosa Donor 29	rectum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links