Variant report

Variant	rs12877288
Chromosome Location	chr13:49172383-49172384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs1009719	0.83[EUR][1000 genomes]
rs11148110	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12050047	0.84[EUR][1000 genomes]
rs12855185	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12859099	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12864882	0.84[EUR][1000 genomes]
rs12876717	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12877954	0.92[EUR][1000 genomes]
rs1359688	0.84[EUR][1000 genomes]
rs1536396	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes]
rs1536397	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs1808060	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1887154	0.87[EUR][1000 genomes]
rs1894255	0.85[CEU][hapmap];0.87[CHB][hapmap];0.82[GIH][hapmap];0.83[JPT][hapmap];0.84[TSI][hapmap];0.93[YRI][hapmap]
rs1951775	0.85[CEU][hapmap]
rs198563	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap]
rs198584	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.84[TSI][hapmap]
rs198590	0.95[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs198604	0.87[CHB][hapmap];0.82[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs198607	0.85[CEU][hapmap];0.87[CHB][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.81[TSI][hapmap]
rs198612	0.90[CEU][hapmap];0.87[CHB][hapmap];0.89[JPT][hapmap]
rs2104532	0.85[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2407093	0.81[EUR][1000 genomes]
rs2407095	0.87[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs3092904	0.80[EUR][1000 genomes]
rs4497565	0.87[EUR][1000 genomes]
rs4635233	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs7139578	0.86[CEU][hapmap]
rs7325719	0.87[EUR][1000 genomes]
rs7332322	0.87[EUR][1000 genomes]
rs7336379	0.80[EUR][1000 genomes]
rs8002098	0.92[EUR][1000 genomes]
rs9316381	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.80[EUR][1000 genomes]
rs9316388	0.95[CEU][hapmap];0.87[CHB][hapmap];0.86[GIH][hapmap];0.89[JPT][hapmap];0.87[TSI][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs9316393	0.83[CEU][hapmap];0.93[CHB][hapmap];0.85[GIH][hapmap];0.83[JPT][hapmap];0.86[YRI][hapmap];0.83[EUR][1000 genomes]
rs9316395	0.86[CEU][hapmap]
rs9316399	0.86[CEU][hapmap]
rs9316407	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9331991	0.80[CHB][hapmap]
rs943278	0.86[CEU][hapmap]
rs943280	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9526481	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9526483	0.82[AFR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9535032	0.86[CEU][hapmap]
rs9535038	0.85[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9535042	0.95[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9535043	0.82[AFR][1000 genomes];0.90[EUR][1000 genomes]
rs9535045	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9535046	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9535049	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9535055	0.84[EUR][1000 genomes]
rs9535056	0.84[EUR][1000 genomes]
rs9535058	0.83[EUR][1000 genomes]
rs9568047	0.85[EUR][1000 genomes]
rs9568049	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9568050	0.89[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs9568051	0.90[EUR][1000 genomes]
rs9568057	0.84[EUR][1000 genomes]
rs9568060	0.84[EUR][1000 genomes]
rs9568063	0.84[EUR][1000 genomes]
rs9595937	0.83[EUR][1000 genomes]
rs9634680	0.93[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs990814	0.86[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12877288	LPAR6	cis	parietal	SCAN
rs12877288	C13orf1	cis	cerebellum	SCAN
rs12877288	ATAD2	trans	parietal	SCAN
rs12877288	ITM2B	cis	lymphoblastoid	seeQTL
rs12877288	ITM2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49161400-49176400	Weak transcription	Right Ventricle	heart
2	chr13:49166200-49173800	Weak transcription	Fetal Kidney	kidney
3	chr13:49168200-49174800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr13:49168400-49175000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
5	chr13:49169800-49177800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr13:49170000-49174800	Weak transcription	HSMM	muscle
7	chr13:49170000-49176600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:49170400-49172400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr13:49170400-49172600	Weak transcription	Pancreas	Pancrea
10	chr13:49170400-49175200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr13:49170400-49176400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr13:49170400-49176600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr13:49170600-49173200	Weak transcription	Hela-S3	cervix
14	chr13:49172200-49172400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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