Variant report

Variant	rs6132843
Chromosome Location	chr20:25532622-25532623
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	chr20:25527993..25531935-chr20:25532103..25536605,5	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11697535	0.94[AMR][1000 genomes]
rs11698047	1.00[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs13045549	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs34056528	0.94[AMR][1000 genomes]
rs35464704	0.89[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35705198	0.94[AMR][1000 genomes]
rs6132841	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6132855	0.88[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]
rs6138578	0.83[ASN][1000 genomes]
rs6138585	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs6138638	0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1067379	chr20:25355484-25593240	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv1060591	chr20:25388781-25628750	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv544223	chr20:25388781-25628750	ZNF genes & repeats Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1067441	chr20:25397566-25615439	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv912828	chr20:25433015-25595175	Weak transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv1062452	chr20:25438025-25590278	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv1066066	chr20:25439367-25588016	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv544224	chr20:25439367-25588016	Genic enhancers ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	nsv912829	chr20:25444242-25595175	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
10	nsv912830	chr20:25449945-25595175	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv912831	chr20:25449945-25595868	Weak transcription Enhancers Strong transcription Genic enhancers ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv994976	chr20:25466406-25593286	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
13	nsv534623	chr20:25466406-25593296	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
14	nsv1062765	chr20:25466482-25556751	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
15	nsv544225	chr20:25466482-25556751	Genic enhancers Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
16	esv2762069	chr20:25506582-25619528	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
17	nsv912832	chr20:25527984-25595175	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25517800-25554600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr20:25521400-25534200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr20:25521600-25565000	Weak transcription	Aorta	Aorta
4	chr20:25524400-25565000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr20:25525000-25535400	Enhancers	Fetal Heart	heart
6	chr20:25526200-25534400	Weak transcription	Brain Substantia Nigra	brain
7	chr20:25526400-25543600	Weak transcription	Fetal Brain Female	brain
8	chr20:25526600-25534200	Weak transcription	Brain Hippocampus Middle	brain
9	chr20:25526600-25540200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr20:25529000-25535600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr20:25529600-25533800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr20:25529600-25534200	Weak transcription	Thymus	Thymus
13	chr20:25529800-25533000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr20:25530000-25532800	Enhancers	H1 Cell Line	embryonic stem cell
15	chr20:25530000-25532800	Enhancers	HUES6 Cell Line	embryonic stem cell
16	chr20:25530200-25532800	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr20:25530200-25532800	Enhancers	iPS-18 Cell Line	embryonic stem cell
18	chr20:25530400-25533400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr20:25530400-25534200	Weak transcription	NHDF-Ad	bronchial
20	chr20:25530400-25534400	Weak transcription	Placenta	Placenta
21	chr20:25530400-25534400	Weak transcription	Pancreas	Pancrea
22	chr20:25530600-25542800	Weak transcription	HSMM	muscle
23	chr20:25530800-25533200	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr20:25530800-25533400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr20:25530800-25534200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr20:25530800-25540000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr20:25531000-25533400	Enhancers	HepG2	liver
28	chr20:25531000-25533800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr20:25531000-25534000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
30	chr20:25531000-25534200	Weak transcription	NHLF	lung
31	chr20:25531000-25534400	Weak transcription	Cortex derived primary cultured neurospheres	brain
32	chr20:25531000-25534400	Weak transcription	Lung	lung
33	chr20:25531000-25534400	Weak transcription	Spleen	Spleen
34	chr20:25531000-25534400	Weak transcription	Hela-S3	cervix
35	chr20:25531000-25554000	Weak transcription	Osteobl	bone
36	chr20:25531200-25534200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr20:25531200-25534200	Weak transcription	Fetal Muscle Trunk	muscle
38	chr20:25531200-25534200	Weak transcription	Fetal Muscle Leg	muscle
39	chr20:25531200-25534400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
40	chr20:25531200-25534400	Weak transcription	Brain Germinal Matrix	brain
41	chr20:25531200-25534400	Weak transcription	Esophagus	oesophagus
42	chr20:25531200-25535000	Enhancers	Colon Smooth Muscle	Colon
43	chr20:25531200-25540200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr20:25531200-25544400	Weak transcription	Fetal Brain Male	brain
45	chr20:25531200-25559600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr20:25531400-25534200	Weak transcription	Adipose Nuclei	Adipose
47	chr20:25531600-25533000	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr20:25531600-25534400	Weak transcription	Right Atrium	heart
49	chr20:25531800-25532800	Enhancers	iPS-15b Cell Line	embryonic stem cell
50	chr20:25531800-25532800	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links