Variant report

Variant	rs9573658
Chromosome Location	chr13:76353522-76353523
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1036869	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1570556	0.84[ASN][1000 genomes]
rs2031241	0.83[ASN][1000 genomes]
rs2120067	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2120068	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2274062	0.91[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4885348	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4885349	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.94[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs618930	0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7320900	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7321748	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7326714	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7331429	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7992526	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7996791	0.85[CEU][hapmap]
rs9530473	0.84[CEU][hapmap];0.83[GIH][hapmap]
rs9544043	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9573659	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9573658	TBC1D4	cis	cerebellum	SCAN
rs9573658	C13orf45	cis	Nerve Tibial	GTEx

Chromatin state (count:46 , 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	chr13:76342400-76357800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr13:76343400-76370800	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr13:76344800-76356800	Weak transcription	Fetal Lung	lung
10	chr13:76346800-76361600	Weak transcription	Duodenum Mucosa	Duodenum
11	chr13:76347400-76358000	Weak transcription	Sigmoid Colon	Sigmoid Colon
12	chr13:76347400-76361400	Weak transcription	HMEC	breast
13	chr13:76347600-76353600	Weak transcription	Esophagus	oesophagus
14	chr13:76347800-76356400	Weak transcription	NH-A	brain
15	chr13:76347800-76356600	Weak transcription	HSMMtube	muscle
16	chr13:76347800-76356800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr13:76347800-76361400	Weak transcription	Gastric	stomach
18	chr13:76348200-76354400	Weak transcription	Fetal Intestine Large	intestine
19	chr13:76348400-76356600	Weak transcription	Liver	Liver
20	chr13:76348600-76355200	Strong transcription	Osteobl	bone
21	chr13:76349000-76356800	Weak transcription	NHLF	lung
22	chr13:76350000-76371000	Weak transcription	Primary T cells fromperipheralblood	blood
23	chr13:76350200-76358000	Weak transcription	Small Intestine	intestine
24	chr13:76350600-76361200	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr13:76351200-76356600	Weak transcription	Pancreatic Islets	Pancreatic Islet
26	chr13:76351400-76354000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr13:76351400-76354600	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:76351400-76356600	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr13:76351400-76360200	Weak transcription	Right Ventricle	heart
30	chr13:76351600-76356600	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr13:76351800-76356800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr13:76352600-76353800	Strong transcription	HSMM	muscle
33	chr13:76352600-76355000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr13:76352600-76355000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr13:76352600-76355200	ZNF genes & repeats	Fetal Intestine Small	intestine
36	chr13:76352800-76353600	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr13:76352800-76353800	Strong transcription	NHDF-Ad	bronchial
38	chr13:76352800-76357200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr13:76353000-76353600	Strong transcription	HepG2	liver
40	chr13:76353000-76354000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr13:76353000-76355200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr13:76353200-76353800	Enhancers	A549	lung
43	chr13:76353400-76356400	Weak transcription	Hela-S3	cervix
44	chr13:76353400-76356600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr13:76353400-76362800	Weak transcription	Lung	lung
46	chr13:76353400-76370600	Weak transcription	Primary T cells from cord blood	blood

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