Variant report

Variant	rs13035357
Chromosome Location	chr2:99752246-99752247
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	chr2:99751840..99754191-chr2:99952770..99955283,2	MCF-7	breast:
2	chr2:99737056..99739481-chr2:99752049..99753991,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000158417	Chromatin interaction
ENSG00000115514	Chromatin interaction

Extended variants
information (count: 57 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10167390	0.84[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs10170063	0.86[AFR][1000 genomes]
rs11123770	0.81[EUR][1000 genomes]
rs1115756	0.89[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1115757	0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs1133977	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1133978	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11683107	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11683188	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11688004	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692336	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11692669	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11895749	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12470471	0.91[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs12613624	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12619780	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12987548	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13000731	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13008171	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13012481	0.84[EUR][1000 genomes]
rs13023501	0.80[AFR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13033012	0.87[AFR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1453563	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1563106	0.85[ASN][1000 genomes]
rs1563107	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs1563108	0.85[ASN][1000 genomes]
rs17708262	0.94[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs17759607	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2084988	0.84[AFR][1000 genomes]
rs2516830	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2516833	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2516835	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2632283	0.99[AFR][1000 genomes];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28648058	0.94[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs34272114	0.99[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4347885	0.86[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4850897	0.99[AFR][1000 genomes];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4851183	0.81[AFR][1000 genomes]
rs4851188	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542866	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6542868	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6708878	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6724476	0.81[AFR][1000 genomes]
rs6727749	0.87[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6735801	0.88[AFR][1000 genomes]
rs6737257	0.90[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs6753650	0.83[ASN][1000 genomes]
rs6754843	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs720229	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7570657	0.88[AFR][1000 genomes]
rs7571390	0.81[AFR][1000 genomes]
rs7605734	0.88[AFR][1000 genomes]
rs7606635	0.88[AFR][1000 genomes]
rs7608938	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv535839	chr2:99742621-99793747	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs13035357	TSGA10	cis	lung	GTEx
rs13035357	TSGA10	cis	Thyroid	GTEx
rs13035357	LIPT1	Cis_1M	lymphoblastoid	RTeQTL
rs13035357	MITD1	cis	Esophagus Mucosa	GTEx
rs13035357	TSGA10	Cis_1M	lymphoblastoid	RTeQTL
rs13035357	MITD1	Cis_1M	lymphoblastoid	RTeQTL
rs13035357	TSGA10	cis	Esophagus Mucosa	GTEx

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:99742800-99757200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:99743200-99757000	Weak transcription	Small Intestine	intestine
3	chr2:99743400-99756400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:99743400-99756600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr2:99743400-99756800	Weak transcription	Brain Cingulate Gyrus	brain
6	chr2:99748800-99753000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr2:99750200-99756200	Weak transcription	Brain Hippocampus Middle	brain
8	chr2:99751000-99756600	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:99751200-99756800	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr2:99751600-99755600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr2:99751800-99756400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr2:99752200-99753600	Weak transcription	Monocytes-CD14+_RO01746	blood

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