Variant report

Variant	rs10002814
Chromosome Location	chr4:129162533-129162534
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11098953	0.95[EUR][1000 genomes]
rs11098954	1.00[CEU][hapmap];0.93[EUR][1000 genomes]
rs11733374	0.91[ASN][1000 genomes]
rs12505763	0.86[CHD][hapmap];0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs12510308	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs12511648	0.92[ASN][1000 genomes]
rs13103695	0.91[ASN][1000 genomes]
rs1403125	0.91[ASN][1000 genomes]
rs1522432	0.91[ASN][1000 genomes]
rs1851400	0.86[ASN][1000 genomes]
rs1948506	0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]
rs2140107	0.94[ASN][1000 genomes]
rs28609279	0.94[EUR][1000 genomes]
rs34174952	0.91[ASN][1000 genomes]
rs4016	0.80[CEU][hapmap]
rs430431	0.80[CEU][hapmap]
rs4624668	0.91[ASN][1000 genomes]
rs4975180	0.80[CEU][hapmap]
rs4975220	0.85[CEU][hapmap];0.84[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs4975299	0.81[EUR][1000 genomes]
rs4975300	0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60515985	0.84[ASN][1000 genomes]
rs6534674	0.94[ASN][1000 genomes]
rs6534675	0.94[ASN][1000 genomes]
rs6816625	0.95[EUR][1000 genomes]
rs6849992	0.94[EUR][1000 genomes]
rs7679633	0.91[ASN][1000 genomes]
rs7688852	0.92[ASN][1000 genomes]
rs7691103	0.81[AMR][1000 genomes];0.91[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	esv3390887	chr4:128932563-129207255	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10002814	LARP2	cis	multi-tissue	Pritchard

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:129161200-129162800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr4:129161200-129165600	Enhancers	Placenta	Placenta
3	chr4:129161400-129162800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr4:129161600-129162600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr4:129161600-129163600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:129161600-129163800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr4:129161600-129163800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr4:129161600-129163800	Enhancers	HMEC	breast
9	chr4:129161600-129163800	Enhancers	HSMM	muscle
10	chr4:129161800-129162600	Enhancers	NHEK	skin
11	chr4:129161800-129162800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr4:129161800-129163200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr4:129161800-129163800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr4:129161800-129163800	Enhancers	NHLF	lung
15	chr4:129161800-129164000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr4:129161800-129164000	Enhancers	Osteobl	bone
17	chr4:129162000-129162600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr4:129162000-129162600	Enhancers	HepG2	liver
19	chr4:129162000-129163200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
20	chr4:129162000-129163400	Enhancers	Adipose Nuclei	Adipose
21	chr4:129162200-129162600	Enhancers	NH-A	brain
22	chr4:129162200-129163200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr4:129162200-129163200	Enhancers	Fetal Intestine Small	intestine
24	chr4:129162200-129163800	Enhancers	Hela-S3	cervix
25	chr4:129162200-129164000	Enhancers	Breast Myoepithelial Primary Cells	Breast
26	chr4:129162400-129162600	Enhancers	Muscle Satellite Cultured Cells	--
27	chr4:129162400-129162600	Enhancers	HSMMtube	muscle
28	chr4:129162400-129162800	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
29	chr4:129162400-129162800	Flanking Active TSS	NHDF-Ad	bronchial
30	chr4:129162400-129163200	Weak transcription	Placenta Amnion	Placenta Amnion
31	chr4:129162400-129163400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr4:129162400-129163600	Enhancers	A549	lung

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