Variant report

Variant	rs13008496
Chromosome Location	chr2:99723111-99723112
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:99721431..99723129-chr2:99723599..99725832,2	MCF-7	breast:

Extended variants
information (count: 142 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:140)

rs_ID	r²[population]
rs10165534	0.83[ASN][1000 genomes]
rs10179043	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.85[ASN][1000 genomes]
rs10190421	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs10196680	0.83[ASN][1000 genomes]
rs1044575	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10865029	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123761	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123762	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11123763	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123764	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11123765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11123766	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1133977	0.91[CEU][hapmap]
rs11674894	0.86[CEU][hapmap]
rs11677247	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11677321	0.82[ASN][1000 genomes]
rs11678456	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11683107	0.91[CEU][hapmap]
rs11683188	0.86[CEU][hapmap]
rs11684507	0.85[AFR][1000 genomes]
rs11684610	0.81[AFR][1000 genomes]
rs11685759	0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11688004	0.91[CEU][hapmap]
rs11689265	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs11692699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11693427	0.81[AFR][1000 genomes]
rs11695379	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11695751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs11883676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11890338	0.86[AFR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11900670	0.87[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12464710	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs12467679	0.83[ASN][1000 genomes]
rs12468807	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12473029	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12477754	0.83[ASN][1000 genomes]
rs12477978	0.83[AFR][1000 genomes]
rs12613624	0.91[CEU][hapmap]
rs12619780	0.83[AFR][1000 genomes]
rs12621007	0.80[ASN][1000 genomes]
rs12992218	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12992930	0.81[EUR][1000 genomes]
rs12995473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12999417	0.95[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap]
rs13004491	0.84[AFR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13008171	0.91[CEU][hapmap]
rs13009147	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13018891	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13020339	0.81[EUR][1000 genomes]
rs13022329	0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13023744	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13030961	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs13033012	0.91[CEU][hapmap]
rs13035311	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1349778	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs1349779	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs13798	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1453561	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1453562	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1453563	0.91[CEU][hapmap]
rs1580068	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17708218	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs17759607	0.91[CEU][hapmap]
rs1993230	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2045057	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs2171359	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2171362	0.80[AFR][1000 genomes]
rs2309524	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs2309581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2516827	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2516828	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2516829	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2516830	0.91[CEU][hapmap]
rs2516832	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2516834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2516835	0.91[CEU][hapmap]
rs2516836	0.83[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs2632260	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2632261	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2632277	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2632283	0.91[CEU][hapmap]
rs2632284	0.82[ASN][1000 genomes]
rs2964969	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2969379	0.82[ASN][1000 genomes]
rs34252185	0.90[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34766932	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs36071868	0.89[AFR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4324365	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4340581	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4402818	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4588238	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4622780	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs4850897	0.91[CEU][hapmap]
rs4851184	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs4851187	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs4851188	0.91[CEU][hapmap]
rs6542852	0.80[ASN][1000 genomes]
rs6542858	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6542863	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542864	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6542865	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6542866	0.91[CEU][hapmap]
rs6542868	0.91[CEU][hapmap]
rs6542869	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6542870	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6704766	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6708576	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6712704	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6717723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs6717729	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6726618	0.84[AFR][1000 genomes]
rs6727749	0.91[CEU][hapmap]
rs6733285	0.91[CEU][hapmap]
rs6736064	0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6739579	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6741772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap]
rs6743355	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6751927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs6753063	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6753650	0.82[AFR][1000 genomes]
rs6756650	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6757019	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs6757661	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6759354	0.83[ASN][1000 genomes]
rs720228	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs720229	0.91[CEU][hapmap]
rs7349217	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs7558004	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7558239	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.80[ASN][1000 genomes]
rs7572660	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7577477	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7584809	0.90[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7604557	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs7605843	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8179690	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs896886	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs9308816	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs972768	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs9808541	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs9941561	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]

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	nsv1007718	chr2:99542281-99729107	Bivalent/Poised TSS Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	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

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs13008496	LIPT1	cis	lesional skin	skin_eQTL
rs13008496	MITD1	cis	Nerve Tibial	GTEx
rs13008496	TSGA10	cis	Thyroid	GTEx
rs13008496	LIPT1	cis	uninvolved skin	skin_eQTL
rs13008496	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs13008496	TSGA10	cis	multi-tissue	Pritchard
rs13008496	TSGA10	cis	lung	GTEx
rs13008496	LIPT1	cis	normal skin	skin_eQTL
rs13008496	TSGA10	cis	Esophagus Mucosa	GTEx
rs13008496	TSGA10	cis	cerebellar cortex	BrainEAC
rs13008496	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs13008496	LIPT1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:14 , 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	chr2:99718200-99729400	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:99718400-99723800	Weak transcription	Ovary	ovary
4	chr2:99718400-99724200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr2:99718600-99739600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr2:99718800-99723400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr2:99718800-99723400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr2:99718800-99727200	Weak transcription	Primary T cells from cord blood	blood
9	chr2:99719800-99724600	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:99722000-99723800	Enhancers	Primary monocytes fromperipheralblood	blood
11	chr2:99722000-99723800	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr2:99722000-99723800	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr2:99722800-99723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
14	chr2:99722800-99723800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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