Variant report

Variant	rs583368
Chromosome Location	chr13:76350821-76350822
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs2025341	0.92[ASN][1000 genomes]
rs2273997	0.92[ASN][1000 genomes]
rs474240	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs527731	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs552441	0.90[ASN][1000 genomes]
rs598500	0.95[ASN][1000 genomes]
rs658746	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs660942	1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs668008	0.95[ASN][1000 genomes]
rs674611	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7335067	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9544044	0.85[ASN][1000 genomes]
rs9593129	0.93[ASN][1000 genomes]
rs9593133	0.92[ASN][1000 genomes]
rs9600555	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs9600556	0.93[ASN][1000 genomes]
rs9600558	1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9600561	1.00[JPT][hapmap];0.80[ASN][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	nsv949152	chr13:76211453-76366622	Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs583368	BTF3L1	cis	parietal	SCAN

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76323800-76356600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr13:76338000-76356800	Weak transcription	Brain Anterior Caudate	brain
3	chr13:76338000-76362800	Weak transcription	Fetal Stomach	stomach
4	chr13:76338600-76356600	Weak transcription	Left Ventricle	heart
5	chr13:76338800-76371000	Weak transcription	Fetal Thymus	thymus
6	chr13:76340000-76363600	Weak transcription	Thymus	Thymus
7	chr13:76341800-76352800	Weak transcription	Primary T cells from cord blood	blood
8	chr13:76342400-76357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr13:76344800-76356800	Weak transcription	Fetal Lung	lung
11	chr13:76345200-76351000	Weak transcription	Placenta	Placenta
12	chr13:76345800-76352800	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr13:76346800-76351000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:76346800-76361600	Weak transcription	Duodenum Mucosa	Duodenum
15	chr13:76347400-76358000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr13:76347400-76361400	Weak transcription	HMEC	breast
17	chr13:76347600-76353600	Weak transcription	Esophagus	oesophagus
18	chr13:76347800-76351000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
19	chr13:76347800-76352600	Weak transcription	Hela-S3	cervix
20	chr13:76347800-76356400	Weak transcription	NH-A	brain
21	chr13:76347800-76356600	Weak transcription	HSMMtube	muscle
22	chr13:76347800-76356800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr13:76347800-76361400	Weak transcription	Gastric	stomach
24	chr13:76348200-76351000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr13:76348200-76354400	Weak transcription	Fetal Intestine Large	intestine
26	chr13:76348400-76351800	Strong transcription	HSMM	muscle
27	chr13:76348400-76352800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr13:76348400-76353000	Weak transcription	HepG2	liver
29	chr13:76348400-76356600	Weak transcription	Liver	Liver
30	chr13:76348600-76355200	Strong transcription	Osteobl	bone
31	chr13:76348800-76353000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr13:76349000-76356800	Weak transcription	NHLF	lung
33	chr13:76349200-76352600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:76349800-76351200	Enhancers	HUVEC	blood vessel
35	chr13:76349800-76351400	Enhancers	Fetal Heart	heart
36	chr13:76349800-76351400	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr13:76349800-76351600	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
39	chr13:76350200-76358000	Weak transcription	Small Intestine	intestine
40	chr13:76350400-76351200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:76350400-76351600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr13:76350600-76351200	Enhancers	Stomach Mucosa	stomach
43	chr13:76350600-76351400	Enhancers	A549	lung
44	chr13:76350600-76352600	Weak transcription	Fetal Intestine Small	intestine
45	chr13:76350600-76361200	Weak transcription	Skeletal Muscle Male	skeletal muscle
46	chr13:76350800-76351200	Enhancers	Pancreatic Islets	Pancreatic Islet
47	chr13:76350800-76351200	Genic enhancers	NHDF-Ad	bronchial
48	chr13:76350800-76351400	Enhancers	Rectal Mucosa Donor 31	rectum

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