Variant report

Variant	rs61961487
Chromosome Location	chr13:50365248-50365249
allele	C/T
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:50365172..50367900-chr13:50655465..50657230,2	K562	blood:
2	chr13:50262508..50268089-chr13:50363531..50368771,13	MCF-7	breast:
3	chr13:50363329..50366279-chr13:50509762..50511637,2	MCF-7	breast:
4	chr13:50261767..50269137-chr13:50365068..50368535,12	MCF-7	breast:
5	chr13:50365136..50367359-chr13:50509492..50511604,3	MCF-7	breast:
6	chr13:50253326..50254069-chr13:50365169..50365855,3	MCF-7	breast:
7	chr13:50365087..50367801-chr13:50569333..50572997,5	MCF-7	breast:
8	chr13:50363476..50366040-chr13:51498906..51500626,2	K562	blood:
9	chr13:50363308..50365589-chr13:50370131..50372850,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000176124	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000123178	Chromatin interaction
ENSG00000123179	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000204977	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1008939	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12019576	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35526541	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3742096	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58303577	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61961485	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7324563	0.83[EUR][1000 genomes]
rs7328465	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7982919	0.81[EUR][1000 genomes]
rs7983049	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7996689	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9316478	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9526603	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9526606	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9535318	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535320	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535323	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9535325	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535327	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9535331	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9535346	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9535360	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535361	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9535362	0.83[EUR][1000 genomes]
rs9535366	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs957474	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv900072	chr13:50266109-50381016	Weak transcription ZNF genes & repeats Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv900073	chr13:50286218-50381016	Enhancers Active TSS Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	esv1818134	chr13:50306897-50374102	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv900074	chr13:50317104-50381016	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv900075	chr13:50331992-50376858	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
6	esv3421253	chr13:50364151-50368649	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50349600-50365400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr13:50349600-50365400	Weak transcription	Lung	lung
3	chr13:50354200-50365400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr13:50354400-50365400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr13:50358400-50365600	Weak transcription	Gastric	stomach
6	chr13:50362800-50365600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr13:50363000-50365400	Enhancers	Primary T helper cells fromperipheralblood	blood
8	chr13:50363400-50365800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr13:50363600-50365400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr13:50363600-50365400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr13:50363800-50365400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:50363800-50365800	Enhancers	Small Intestine	intestine
13	chr13:50364000-50367600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr13:50364200-50365400	Flanking Active TSS	Hela-S3	cervix
15	chr13:50364200-50367800	Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr13:50364400-50365400	Enhancers	Primary B cells from peripheral blood	blood
17	chr13:50364400-50365400	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr13:50364600-50365400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:50364600-50365400	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
20	chr13:50364600-50365400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr13:50364600-50365400	Weak transcription	Esophagus	oesophagus
22	chr13:50364600-50365400	Weak transcription	Left Ventricle	heart
23	chr13:50364600-50365400	Weak transcription	Pancreas	Pancrea
24	chr13:50364600-50365400	Weak transcription	Spleen	Spleen
25	chr13:50364600-50365600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr13:50364600-50365800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr13:50364600-50365800	Flanking Active TSS	Fetal Brain Female	brain
28	chr13:50364600-50365800	Enhancers	Placenta Amnion	Placenta Amnion
29	chr13:50364600-50366000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr13:50364600-50366000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
31	chr13:50364600-50367600	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr13:50364600-50367800	Active TSS	Aorta	Aorta
33	chr13:50364600-50368000	Active TSS	H1 Cell Line	embryonic stem cell
34	chr13:50364600-50368000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr13:50364600-50368000	Active TSS	Pancreatic Islets	Pancreatic Islet
36	chr13:50364800-50365400	Enhancers	Primary T cells from cord blood	blood
37	chr13:50364800-50365400	Flanking Active TSS	Brain Germinal Matrix	brain
38	chr13:50364800-50365400	Weak transcription	Ovary	ovary
39	chr13:50364800-50365400	Flanking Active TSS	Osteobl	bone
40	chr13:50364800-50365600	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr13:50364800-50365600	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
42	chr13:50364800-50365600	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
43	chr13:50364800-50365600	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr13:50364800-50365600	Flanking Active TSS	NHEK	skin
45	chr13:50364800-50365800	Flanking Active TSS	HUVEC	blood vessel
46	chr13:50364800-50365800	Flanking Active TSS	NH-A	brain
47	chr13:50364800-50366000	Flanking Active TSS	Adipose Nuclei	Adipose
48	chr13:50364800-50366000	Flanking Active TSS	Liver	Liver
49	chr13:50364800-50366600	Active TSS	Right Atrium	heart
50	chr13:50364800-50367600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung

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