Variant report

Variant	rs10519613
Chromosome Location	chr4:142654084-142654085
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1021446	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519612	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10519614	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508866	0.92[MKK][hapmap]
rs13106911	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13107813	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13122930	0.83[CHD][hapmap]
rs13139573	0.81[CHD][hapmap]
rs13150149	0.93[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs1389102	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17007636	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17007642	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17461899	0.88[EUR][1000 genomes]
rs1907949	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2131412	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2222277	0.88[EUR][1000 genomes]
rs2291596	0.86[CHD][hapmap]
rs2322301	0.81[CHD][hapmap]
rs33979009	0.90[ASN][1000 genomes]
rs34376144	0.87[ASN][1000 genomes]
rs34468566	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35514738	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35636124	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35964658	0.90[ASN][1000 genomes]
rs3775596	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3775597	1.00[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58934440	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62325678	0.86[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs62327424	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67013870	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs68003574	0.88[ASN][1000 genomes]
rs6819823	0.81[CHD][hapmap]
rs71608457	0.83[ASN][1000 genomes]
rs957077	1.00[CEU][hapmap];0.91[MKK][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv880173	chr4:142355535-142666106	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3401979	chr4:142434442-142803321	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1018949	chr4:142451823-142732365	Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv1030822	chr4:142487721-142706053	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv1027004	chr4:142487721-143007320	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv498005	chr4:142515689-143502988	Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3448093	chr4:142612197-142704695	Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519613	TBC1D9	cis	parietal	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:142608800-142655000	Weak transcription	Gastric	stomach
2	chr4:142629400-142654600	Weak transcription	Esophagus	oesophagus
3	chr4:142629400-142655000	Weak transcription	Spleen	Spleen
4	chr4:142629600-142657600	Weak transcription	Right Ventricle	heart
5	chr4:142634800-142656200	Weak transcription	Pancreas	Pancrea
6	chr4:142639600-142655000	Weak transcription	Primary B cells from cord blood	blood
7	chr4:142639600-142657400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr4:142641400-142655000	Weak transcription	Lung	lung
9	chr4:142641800-142654200	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr4:142644800-142654400	Weak transcription	GM12878-XiMat	blood
11	chr4:142644800-142655800	Weak transcription	Rectal Mucosa Donor 31	rectum
12	chr4:142646600-142655800	Weak transcription	Small Intestine	intestine
13	chr4:142649800-142655400	Weak transcription	Fetal Intestine Large	intestine
14	chr4:142651000-142654600	Strong transcription	Duodenum Smooth Muscle	Duodenum
15	chr4:142651000-142654600	Strong transcription	Skeletal Muscle Female	skeletal muscle
16	chr4:142651000-142654800	Strong transcription	Monocytes-CD14+_RO01746	blood
17	chr4:142651400-142654200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
18	chr4:142651400-142655000	Weak transcription	Rectal Smooth Muscle	rectum
19	chr4:142651600-142655600	Weak transcription	A549	lung
20	chr4:142651800-142654800	Strong transcription	Aorta	Aorta
21	chr4:142652000-142656800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr4:142652200-142656200	Weak transcription	Sigmoid Colon	Sigmoid Colon
23	chr4:142652400-142656000	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr4:142652400-142656400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr4:142652400-142656400	Weak transcription	HSMM	muscle
26	chr4:142652800-142655600	Weak transcription	Adipose Nuclei	Adipose
27	chr4:142652800-142656600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr4:142653000-142656000	Weak transcription	Liver	Liver
29	chr4:142653000-142659200	Weak transcription	Left Ventricle	heart
30	chr4:142653600-142656200	Weak transcription	Skeletal Muscle Male	skeletal muscle
31	chr4:142653800-142656000	Weak transcription	Duodenum Mucosa	Duodenum
32	chr4:142653800-142658000	Weak transcription	Stomach Smooth Muscle	stomach
33	chr4:142654000-142654600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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