Variant report

Variant	rs6126946
Chromosome Location	chr20:52389548-52389549
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52387876..52389720-chr20:55843300..55845987,2	MCF-7	breast:
2	chr20:52386895..52389941-chr20:55840050..55842115,3	MCF-7	breast:
3	chr12:51045033..51047278-chr20:52389082..52391605,2	MCF-7	breast:
4	chr20:52380779..52382680-chr20:52389326..52391333,2	K562	blood:
5	chr17:57930644..57932261-chr20:52388672..52392244,3	MCF-7	breast:
6	chr20:49346453..49349667-chr20:52388930..52390587,3	MCF-7	breast:
7	chr20:52389038..52391230-chr3:133302183..133304209,2	MCF-7	breast:
8	chr20:52388338..52391629-chr20:55836621..55838801,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000124171	Chromatin interaction
ENSG00000226308	Chromatin interaction
ENSG00000101144	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs36080156	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6123313	0.89[ASN][1000 genomes]
rs6126949	0.91[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	esv3412883	chr20:52176349-52393416	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	250 gene(s)	inside rSNPs	diseases
2	nsv834007	chr20:52213864-52404557	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	174 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:52380000-52391000	Weak transcription	Pancreas	Pancrea
2	chr20:52380800-52389600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr20:52380800-52390000	Weak transcription	Placenta Amnion	Placenta Amnion
4	chr20:52381000-52394600	Weak transcription	Right Atrium	heart
5	chr20:52381200-52390000	Weak transcription	Duodenum Smooth Muscle	Duodenum
6	chr20:52381200-52390000	Weak transcription	Fetal Kidney	kidney
7	chr20:52381400-52390000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr20:52381400-52390000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr20:52384400-52390000	Weak transcription	Stomach Mucosa	stomach
10	chr20:52384400-52394800	Weak transcription	Duodenum Mucosa	Duodenum
11	chr20:52384800-52389800	Weak transcription	Liver	Liver
12	chr20:52385400-52392400	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr20:52385800-52389800	Weak transcription	Osteobl	bone
14	chr20:52385800-52390000	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr20:52385800-52390000	Enhancers	HepG2	liver
16	chr20:52386000-52389800	Weak transcription	Small Intestine	intestine
17	chr20:52386000-52390000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr20:52386000-52390000	Weak transcription	Fetal Intestine Small	intestine
19	chr20:52386000-52390200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr20:52386000-52390200	Enhancers	A549	lung
21	chr20:52386200-52389600	Weak transcription	Muscle Satellite Cultured Cells	--
22	chr20:52386200-52390000	Weak transcription	Fetal Lung	lung
23	chr20:52388600-52390000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr20:52388800-52389800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr20:52388800-52390400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr20:52388800-52390400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr20:52388800-52390800	Enhancers	NH-A	brain
28	chr20:52388800-52392000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr20:52389000-52390800	Enhancers	HSMM	muscle
30	chr20:52389000-52391800	Enhancers	HSMMtube	muscle
31	chr20:52389000-52392000	Enhancers	HMEC	breast
32	chr20:52389000-52392000	Enhancers	NHEK	skin
33	chr20:52389200-52389600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr20:52389200-52389600	Weak transcription	NHLF	lung
35	chr20:52389200-52389800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr20:52389200-52390000	Weak transcription	Fetal Stomach	stomach
37	chr20:52389400-52389600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr20:52389400-52390800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr20:52389400-52390800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr20:52389400-52391400	Enhancers	Placenta	Placenta
41	chr20:52389400-52392000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr20:52389400-52392200	Enhancers	Breast Myoepithelial Primary Cells	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links