Variant report

Variant	rs11099829
Chromosome Location	chr4:152727299-152727300
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs10001603	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10013612	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10016160	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10222838	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10222925	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11099828	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11723227	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12331037	0.81[GIH][hapmap]
rs12502446	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12503677	0.80[ASN][1000 genomes]
rs12641433	0.92[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs13108359	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13119490	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13121178	0.93[EUR][1000 genomes]
rs13121190	0.89[EUR][1000 genomes]
rs13138986	0.80[JPT][hapmap]
rs13139327	0.90[EUR][1000 genomes]
rs13145446	0.93[EUR][1000 genomes]
rs13147021	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13149588	0.80[JPT][hapmap]
rs1366907	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1397683	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1429558	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1429559	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17360475	0.81[GIH][hapmap]
rs1877185	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877186	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1877188	0.88[CEU][hapmap]
rs2089811	0.96[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2175409	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2303866	0.94[JPT][hapmap]
rs2406973	0.92[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.85[TSI][hapmap]
rs34615528	0.82[AFR][1000 genomes]
rs3805356	0.96[CEU][hapmap];0.91[CHB][hapmap];0.91[GIH][hapmap];0.84[JPT][hapmap];0.86[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3828546	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4399967	0.90[EUR][1000 genomes]
rs4554052	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643789	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4696109	0.81[GIH][hapmap]
rs4696110	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4696290	0.92[CEU][hapmap];0.86[CHB][hapmap];0.91[GIH][hapmap];0.89[JPT][hapmap];0.82[MEX][hapmap];0.85[TSI][hapmap];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4696293	0.85[GIH][hapmap]
rs4696295	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4696296	0.83[ASN][1000 genomes]
rs4696297	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs58751443	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs59350867	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61308159	0.90[EUR][1000 genomes]
rs6535816	0.92[CEU][hapmap];0.86[CHB][hapmap];0.89[JPT][hapmap];0.81[ASN][1000 genomes]
rs6535818	0.81[GIH][hapmap]
rs6535819	0.81[GIH][hapmap]
rs6535822	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6836954	0.81[AFR][1000 genomes]
rs6847844	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6849111	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6855883	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6857073	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7654294	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7669465	0.92[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap]
rs7669761	0.92[CEU][hapmap];0.84[GIH][hapmap];0.85[TSI][hapmap]
rs7669977	0.81[GIH][hapmap]
rs7675818	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs867800	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9996320	0.80[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	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs11099829	PET112L	cis	lymphoblastoid	seeQTL
rs11099829	PET112L	cis	multi-tissue	Pritchard
rs11099829	PET112L	cis	parietal	SCAN
rs11099829	PET112L	cis	cerebellum	SCAN
rs11099829	FAM160A1	cis	cerebellum	SCAN
rs11099829	PET112L	cis	Lymphoblastoid	GTEx

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152719200-152727400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr4:152720200-152728400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr4:152720200-152728600	Weak transcription	Right Atrium	heart
4	chr4:152721000-152729000	Weak transcription	Left Ventricle	heart
5	chr4:152721200-152729200	Weak transcription	H1 Cell Line	embryonic stem cell
6	chr4:152721200-152731400	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr4:152721400-152727600	Weak transcription	HUES48 Cell Line	embryonic stem cell
8	chr4:152721400-152727800	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr4:152721600-152727600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr4:152722400-152727800	Weak transcription	Fetal Intestine Large	intestine
11	chr4:152722400-152727800	Weak transcription	Fetal Intestine Small	intestine
12	chr4:152723600-152729000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr4:152723800-152729200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr4:152724000-152729800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr4:152725000-152727400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr4:152725000-152728600	Enhancers	HSMM	muscle
17	chr4:152725800-152727800	Enhancers	NH-A	brain
18	chr4:152726000-152727600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
19	chr4:152726000-152731800	Enhancers	Fetal Heart	heart
20	chr4:152726200-152727400	Weak transcription	Osteobl	bone
21	chr4:152726200-152727600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr4:152726200-152731200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr4:152726400-152727400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr4:152726400-152732000	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr4:152726800-152727800	Weak transcription	NHLF	lung
26	chr4:152726800-152730000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr4:152727200-152729400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr4:152727200-152730000	Enhancers	HSMMtube	muscle

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