Variant report

Variant	rs345353
Chromosome Location	chr4:86784168-86784169
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10034094	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11097077	0.83[ASN][1000 genomes]
rs11097078	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11947357	0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs12152604	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12152609	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397377	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1397378	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473012	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473013	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473014	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1473015	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1510583	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1606017	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17011103	0.91[ASN][1000 genomes]
rs180778	0.86[ASN][1000 genomes]
rs2601832	0.83[ASN][1000 genomes]
rs2601833	0.86[ASN][1000 genomes]
rs2601869	1.00[CEU][hapmap];0.81[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28641527	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2869406	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs28698740	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28770594	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28814882	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs345326	0.82[CHD][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs345327	0.82[CHD][hapmap];0.93[JPT][hapmap];0.87[ASN][1000 genomes]
rs345331	0.89[EUR][1000 genomes]
rs345332	0.89[EUR][1000 genomes]
rs345335	0.86[ASN][1000 genomes]
rs345336	0.89[EUR][1000 genomes]
rs345339	0.86[ASN][1000 genomes]
rs345348	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs345356	0.89[EUR][1000 genomes]
rs345360	1.00[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs345361	0.84[ASN][1000 genomes]
rs4420970	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4423865	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693130	0.81[EUR][1000 genomes]
rs4693747	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693748	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4693749	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]
rs58201469	0.86[ASN][1000 genomes]
rs62315465	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62315498	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6820090	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6834349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6840367	0.85[EUR][1000 genomes]
rs72980816	0.86[ASN][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs345353	THAP9	cis	parietal	SCAN

Chromatin state (count:39 , 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	chr4:86776000-86790400	Weak transcription	Right Atrium	heart
4	chr4:86779800-86800200	Weak transcription	Primary B cells from cord blood	blood
5	chr4:86780400-86787600	Weak transcription	Colon Smooth Muscle	Colon
6	chr4:86780400-86790800	Weak transcription	Gastric	stomach
7	chr4:86780800-86785800	Enhancers	Stomach Mucosa	stomach
8	chr4:86781400-86787400	Weak transcription	HSMM	muscle
9	chr4:86781600-86787600	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr4:86781800-86787200	Weak transcription	HSMMtube	muscle
11	chr4:86781800-86787400	Weak transcription	Fetal Muscle Leg	muscle
12	chr4:86781800-86787400	Enhancers	NHDF-Ad	bronchial
13	chr4:86781800-86787600	Weak transcription	NHLF	lung
14	chr4:86781800-86787800	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr4:86781800-86789000	Weak transcription	Small Intestine	intestine
16	chr4:86781800-86790400	Weak transcription	NH-A	brain
17	chr4:86782000-86785200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr4:86782000-86787000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
19	chr4:86782400-86788400	Weak transcription	Stomach Smooth Muscle	stomach
20	chr4:86782600-86787400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:86782600-86787400	Weak transcription	Aorta	Aorta
22	chr4:86782600-86787600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:86782800-86785400	Enhancers	Fetal Kidney	kidney
24	chr4:86782800-86787000	Weak transcription	Osteobl	bone
25	chr4:86782800-86791600	Weak transcription	Duodenum Mucosa	Duodenum
26	chr4:86783000-86787000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr4:86783200-86785400	Weak transcription	HUVEC	blood vessel
28	chr4:86783200-86786600	Weak transcription	Fetal Brain Male	brain
29	chr4:86783200-86787200	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr4:86783400-86784200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr4:86783400-86787600	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr4:86783400-86787600	Weak transcription	Fetal Stomach	stomach
33	chr4:86783600-86784200	Enhancers	ES-I3 Cell Line	embryonic stem cell
34	chr4:86783600-86784400	Weak transcription	Primary hematopoietic stem cells	blood
35	chr4:86783600-86786000	Enhancers	Primary B cells from peripheral blood	blood
36	chr4:86783600-86787200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr4:86783600-86788400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr4:86783800-86786200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr4:86784000-86790200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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