Variant report

Variant	rs61959583
Chromosome Location	chr13:76428594-76428595
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:76428110-76429062	HepG2	liver:	n/a	n/a

Variant related genes	Relation type
LMO7	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12427729	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12428746	0.83[AMR][1000 genomes]
rs12430940	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs17065074	0.82[ASN][1000 genomes]
rs17065145	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2120060	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2120061	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2165774	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2241913	0.82[ASN][1000 genomes]
rs2296093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3736858	0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3759445	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs3783025	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3825439	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs41287008	0.95[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4885357	0.85[AMR][1000 genomes]
rs9318380	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9530471	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9544047	0.91[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs9544049	0.95[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9544050	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9544051	0.95[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9544053	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9544056	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9544059	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832646	chr13:76300428-76483102	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	esv2758333	chr13:76321610-76542003	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	esv2759950	chr13:76321610-76542003	Weak transcription Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv832649	chr13:76424872-76657891	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:92 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76391200-76431600	Strong transcription	Hela-S3	cervix
2	chr13:76394400-76435800	Weak transcription	Colon Smooth Muscle	Colon
3	chr13:76396400-76432000	Weak transcription	Brain Substantia Nigra	brain
4	chr13:76396400-76436800	Weak transcription	Fetal Brain Male	brain
5	chr13:76399000-76433200	Weak transcription	Small Intestine	intestine
6	chr13:76399800-76433000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr13:76406000-76428600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr13:76406000-76429600	Weak transcription	Primary hematopoietic stem cells	blood
9	chr13:76406000-76430600	Strong transcription	Osteobl	bone
10	chr13:76406000-76436800	Strong transcription	Muscle Satellite Cultured Cells	--
11	chr13:76406600-76435000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr13:76408400-76435000	Strong transcription	HSMMtube	muscle
13	chr13:76408400-76435200	Strong transcription	NH-A	brain
14	chr13:76413200-76436800	Strong transcription	NHDF-Ad	bronchial
15	chr13:76413800-76437600	Strong transcription	HSMM	muscle
16	chr13:76414000-76433000	Strong transcription	Liver	Liver
17	chr13:76414200-76433400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
18	chr13:76414400-76435200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr13:76415400-76429200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr13:76416400-76434600	Weak transcription	Spleen	Spleen
21	chr13:76416600-76429800	Weak transcription	Stomach Mucosa	stomach
22	chr13:76417400-76429200	Weak transcription	Adipose Nuclei	Adipose
23	chr13:76417400-76431000	Weak transcription	Brain Cingulate Gyrus	brain
24	chr13:76417400-76433000	Weak transcription	Primary B cells from peripheral blood	blood
25	chr13:76417400-76434600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr13:76417400-76443800	Weak transcription	Fetal Brain Female	brain
27	chr13:76417600-76431400	Weak transcription	Brain Angular Gyrus	brain
28	chr13:76417600-76432600	Weak transcription	Brain Hippocampus Middle	brain
29	chr13:76417600-76434200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
30	chr13:76417600-76436800	Weak transcription	Psoas Muscle	Psoas
31	chr13:76417600-76437800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr13:76417600-76444600	Weak transcription	HMEC	breast
33	chr13:76417800-76433400	Weak transcription	Primary B cells from cord blood	blood
34	chr13:76417800-76438800	Weak transcription	A549	lung
35	chr13:76418800-76432200	Strong transcription	Rectal Mucosa Donor 29	rectum
36	chr13:76421400-76429800	Strong transcription	Placenta	Placenta
37	chr13:76421600-76432200	Strong transcription	Primary T cells from cord blood	blood
38	chr13:76421800-76431600	Strong transcription	Duodenum Mucosa	Duodenum
39	chr13:76421800-76432200	Strong transcription	HepG2	liver
40	chr13:76422000-76431200	Strong transcription	Fetal Intestine Large	intestine
41	chr13:76422800-76430000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr13:76422800-76431800	Strong transcription	Thymus	Thymus
43	chr13:76422800-76432200	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr13:76423000-76431600	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr13:76423200-76428600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
46	chr13:76423200-76428600	Strong transcription	Primary T helper cells fromperipheralblood	blood
47	chr13:76423800-76432200	Strong transcription	Fetal Intestine Small	intestine
48	chr13:76424000-76431800	Weak transcription	Brain Germinal Matrix	brain
49	chr13:76424400-76444200	Weak transcription	Fetal Lung	lung
50	chr13:76425400-76429400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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