Variant report

Variant	rs4693749
Chromosome Location	chr4:86781282-86781283
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10034094	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11097077	0.88[ASN][1000 genomes]
rs11097078	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11947357	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12152604	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12152609	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1397377	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1397378	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473012	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473014	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1473015	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1510583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1606017	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17011103	0.88[ASN][1000 genomes]
rs17011108	0.88[LWK][hapmap]
rs180778	0.90[ASN][1000 genomes]
rs2601832	0.88[ASN][1000 genomes]
rs2601833	0.90[ASN][1000 genomes]
rs2601864	0.86[JPT][hapmap]
rs2601869	1.00[CEU][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28641527	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2869406	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28698740	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28770594	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28814882	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs345326	0.86[CHD][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs345327	0.86[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs345331	0.89[EUR][1000 genomes]
rs345332	0.89[EUR][1000 genomes]
rs345335	0.90[ASN][1000 genomes]
rs345336	0.89[EUR][1000 genomes]
rs345339	0.90[ASN][1000 genomes]
rs345348	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs345353	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs345356	0.89[EUR][1000 genomes]
rs345360	0.96[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs345361	0.89[ASN][1000 genomes]
rs4420970	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4423865	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4693130	0.81[EUR][1000 genomes]
rs4693747	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4693748	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58201469	0.90[ASN][1000 genomes]
rs62315465	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62315498	0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6820090	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6834349	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6840367	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs72980816	0.90[ASN][1000 genomes]
rs9998733	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830000	chr4:86745341-86909059	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4693749	THAP9	cis	parietal	SCAN
rs4693749	HSD17B11	cis	cerebellum	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:86749400-86787600	Weak transcription	Pancreas	Pancrea
2	chr4:86750000-86809200	Weak transcription	Fetal Muscle Trunk	muscle
3	chr4:86760000-86782600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr4:86770000-86783600	Weak transcription	Primary B cells from peripheral blood	blood
5	chr4:86776000-86790400	Weak transcription	Right Atrium	heart
6	chr4:86779600-86783200	Enhancers	HUVEC	blood vessel
7	chr4:86779800-86800200	Weak transcription	Primary B cells from cord blood	blood
8	chr4:86780200-86781400	Enhancers	Fetal Heart	heart
9	chr4:86780200-86781400	Enhancers	HSMM	muscle
10	chr4:86780200-86781600	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr4:86780200-86781800	Enhancers	Fetal Muscle Leg	muscle
12	chr4:86780200-86781800	Enhancers	HSMMtube	muscle
13	chr4:86780200-86781800	Flanking Active TSS	NHDF-Ad	bronchial
14	chr4:86780200-86781800	Enhancers	NHLF	lung
15	chr4:86780200-86782400	Enhancers	Fetal Kidney	kidney
16	chr4:86780400-86787600	Weak transcription	Colon Smooth Muscle	Colon
17	chr4:86780400-86790800	Weak transcription	Gastric	stomach
18	chr4:86780600-86781400	Weak transcription	Fetal Brain Male	brain
19	chr4:86780600-86782800	Enhancers	Fetal Brain Female	brain
20	chr4:86780800-86781600	Enhancers	Brain Germinal Matrix	brain
21	chr4:86780800-86781600	Enhancers	Skeletal Muscle Female	skeletal muscle
22	chr4:86780800-86781800	Enhancers	Adipose Nuclei	Adipose
23	chr4:86780800-86781800	Enhancers	Skeletal Muscle Male	skeletal muscle
24	chr4:86780800-86782000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr4:86780800-86782000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr4:86780800-86783000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:86780800-86783200	Enhancers	Muscle Satellite Cultured Cells	--
28	chr4:86780800-86785800	Enhancers	Stomach Mucosa	stomach
29	chr4:86781000-86781800	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr4:86781000-86782200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr4:86781200-86781400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr4:86781200-86781400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr4:86781200-86781400	Enhancers	Fetal Stomach	stomach
34	chr4:86781200-86781600	Flanking Active TSS	A549	lung
35	chr4:86781200-86781800	Flanking Active TSS	Osteobl	bone
36	chr4:86781200-86782200	Enhancers	Pancreatic Islets	Pancreatic Islet

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