Variant report

Variant	rs6741772
Chromosome Location	chr2:99738961-99738962
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 87 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs10179043	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10190421	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs10865029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11123761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11123765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs1133977	0.92[CEU][hapmap]
rs11674894	0.88[CEU][hapmap]
rs11677247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs11683107	0.92[CEU][hapmap]
rs11683188	0.88[CEU][hapmap]
rs11688004	0.92[CEU][hapmap]
rs11689265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11692699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11695379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11695751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs11883676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12468807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12473029	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs12613624	0.92[CEU][hapmap]
rs12995473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12999417	0.96[CEU][hapmap];0.86[CHB][hapmap];0.88[JPT][hapmap]
rs13008171	0.92[CEU][hapmap]
rs13008496	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs13009147	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap]
rs13018891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13030961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13033012	0.92[CEU][hapmap]
rs13035311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1349778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1349779	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs13798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453562	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs1453563	0.92[CEU][hapmap]
rs1580068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs17708218	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs17759607	0.92[CEU][hapmap]
rs1993230	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2045057	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2171359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2309524	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs2309581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2516827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2516829	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2516830	0.92[CEU][hapmap]
rs2516832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2516834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2516835	0.92[CEU][hapmap]
rs2632260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2632277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2632283	0.92[CEU][hapmap]
rs4324365	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4340581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4588238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4622780	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs4850897	0.92[CEU][hapmap]
rs4851184	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs4851187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs4851188	0.92[CEU][hapmap]
rs6542864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6542866	0.92[CEU][hapmap]
rs6542868	0.92[CEU][hapmap]
rs6704766	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6708576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6717723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6717729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6727749	0.92[CEU][hapmap]
rs6733285	0.92[CEU][hapmap]
rs6751927	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6753063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6756650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6757019	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs720228	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs720229	0.92[CEU][hapmap]
rs7349217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7558239	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs7577477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs7605843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8179690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs896886	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap]
rs9308816	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs972768	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs9808541	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap]
rs9941561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv1013507	chr2:99729047-99861692	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs6741772	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs6741772	LIPT1	cis	lesional skin	skin_eQTL
rs6741772	TSGA10	cis	Thyroid	GTEx
rs6741772	TSGA10	cis	Skin Sun Exposed Lower leg	GTEx
rs6741772	TSGA10	cis	Esophagus Mucosa	GTEx
rs6741772	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs6741772	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs6741772	TSGA10	cis	multi-tissue	Pritchard
rs6741772	LIPT1	cis	uninvolved skin	skin_eQTL
rs6741772	LIPT1	cis	normal skin	skin_eQTL
rs6741772	TSGA10	cis	lung	GTEx
rs6741772	TSGA10	cis	Lymphoblastoid	GTEx

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99718000-99740200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr2:99718600-99739600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr2:99723800-99739600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:99729400-99741600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr2:99735600-99741400	Weak transcription	Brain Angular Gyrus	brain
6	chr2:99736400-99742200	Weak transcription	Pancreas	Pancrea
7	chr2:99738000-99742000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr2:99738200-99742200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:99738600-99742000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr2:99738800-99743800	Weak transcription	HepG2	liver

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