Variant report

Variant	rs13100262
Chromosome Location	chr3:101414102-101414103
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	chr3:101404733..101406490-chr3:101413222..101415957,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1031710	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1056579	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1138818	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11706986	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11710533	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11710805	0.83[ASN][1000 genomes]
rs11711079	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11712748	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11714278	0.87[ASN][1000 genomes]
rs11717046	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11720745	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11914318	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11917569	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11917682	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11919389	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11924013	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11925001	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12629658	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12629954	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12635128	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636557	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12639028	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13059470	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13060963	0.85[ASN][1000 genomes]
rs13061565	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065944	0.84[ASN][1000 genomes]
rs13066768	0.90[ASN][1000 genomes]
rs13068350	0.80[ASN][1000 genomes]
rs13069443	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13077703	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077925	0.90[ASN][1000 genomes]
rs13081846	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13082236	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs13096323	0.80[ASN][1000 genomes]
rs13099674	0.90[ASN][1000 genomes]
rs17411983	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963961	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1963962	0.90[ASN][1000 genomes]
rs2288272	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2303474	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2318090	0.90[ASN][1000 genomes]
rs3094295	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094296	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3094297	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109756	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34181125	0.90[ASN][1000 genomes]
rs34301719	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34376498	0.90[ASN][1000 genomes]
rs34624546	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34883763	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35117343	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35850993	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36002990	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs36060163	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3806653	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806654	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3864012	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55654108	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55821257	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs55859364	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56291106	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59596156	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62282218	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs62282255	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs62284198	0.90[ASN][1000 genomes]
rs62284199	0.90[ASN][1000 genomes]
rs71625262	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7629753	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7645391	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7651406	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651721	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830943	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[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	nsv497784	chr3:101315009-102092989	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
2	nsv997407	chr3:101384031-101611391	Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
3	nsv536675	chr3:101384031-101611391	Weak transcription Flanking Active TSS Strong transcription Enhancers Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs13100262	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs13100262	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101406400-101414400	Weak transcription	Brain Substantia Nigra	brain
2	chr3:101406400-101422200	Weak transcription	Ovary	ovary
3	chr3:101406600-101414600	Weak transcription	Primary B cells from peripheral blood	blood
4	chr3:101406600-101426400	Weak transcription	Fetal Intestine Small	intestine
5	chr3:101406800-101414200	Weak transcription	Brain Cingulate Gyrus	brain
6	chr3:101406800-101414200	Weak transcription	Fetal Kidney	kidney
7	chr3:101406800-101414400	Weak transcription	Brain Anterior Caudate	brain
8	chr3:101406800-101414400	Weak transcription	Fetal Brain Female	brain
9	chr3:101406800-101414600	Weak transcription	Brain Angular Gyrus	brain
10	chr3:101406800-101419200	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:101407000-101422600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr3:101410200-101414600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr3:101410200-101414600	Weak transcription	Primary T helper cells PMA-I stimulated	--
14	chr3:101410200-101420600	Weak transcription	Lung	lung
15	chr3:101410800-101414600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr3:101410800-101415000	Active TSS	iPS-15b Cell Line	embryonic stem cell
17	chr3:101412400-101414400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
18	chr3:101412800-101414400	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr3:101413000-101414800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:101413600-101414600	Enhancers	Fetal Muscle Leg	muscle
21	chr3:101413600-101414800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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