Variant report

Variant	rs1323710
Chromosome Location	chr13:76297887-76297888
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs1323712	0.83[EUR][1000 genomes]
rs1830760	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2025354	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2328953	0.80[EUR][1000 genomes]
rs2328954	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328956	0.83[EUR][1000 genomes]
rs2761398	0.81[EUR][1000 genomes]
rs479824	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs480929	0.81[EUR][1000 genomes]
rs502171	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs504273	0.81[EUR][1000 genomes]
rs508596	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs560069	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607095	0.81[EUR][1000 genomes]
rs61958148	0.87[ASN][1000 genomes]
rs634729	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636505	0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs636580	0.80[EUR][1000 genomes]
rs7324353	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7331527	0.94[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs7999158	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs9530463	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9544034	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9544035	0.83[EUR][1000 genomes]
rs9573627	0.82[AMR][1000 genomes]
rs9600533	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[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	nsv900579	chr13:76244056-76307981	Enhancers Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1091	chr13:76282392-76327906	ZNF genes & repeats Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
4	nsv976261	chr13:76297598-76301199	Weak transcription Genic enhancers Flanking Active TSS Enhancers Strong transcription Active TSS	n/a	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1323710	TBC1D4	cis	cerebellum	SCAN
rs1323710	COMMD6	cis	cerebellum	SCAN
rs1323710	KCTD12	cis	parietal	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:76279400-76308000	Weak transcription	Left Ventricle	heart
2	chr13:76283600-76308000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:76290600-76298000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
4	chr13:76290600-76298200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr13:76290600-76298200	Weak transcription	Aorta	Aorta
6	chr13:76290600-76298400	Weak transcription	Fetal Lung	lung
7	chr13:76290800-76299000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr13:76291600-76298000	Strong transcription	HSMM	muscle
9	chr13:76293800-76298000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr13:76294000-76300200	Weak transcription	HSMMtube	muscle
11	chr13:76294400-76299000	Weak transcription	NHLF	lung
12	chr13:76294800-76321800	Weak transcription	NH-A	brain
13	chr13:76295000-76298000	Weak transcription	Stomach Mucosa	stomach
14	chr13:76297000-76300800	Enhancers	Hela-S3	cervix
15	chr13:76297600-76298800	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:76297600-76299800	Enhancers	NHDF-Ad	bronchial
17	chr13:76297600-76300000	Enhancers	Osteobl	bone
18	chr13:76297800-76298000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:76297800-76298600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:76297800-76298600	Enhancers	Small Intestine	intestine
21	chr13:76297800-76300200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr13:76297800-76300200	Enhancers	Rectal Mucosa Donor 31	rectum
23	chr13:76297800-76300400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr13:76297800-76301400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr13:76297800-76301400	Enhancers	Muscle Satellite Cultured Cells	--

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