Variant report

Variant	rs13069443
Chromosome Location	chr3:101373305-101373306
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101371210..101374028-chr3:101402306..101406539,4	MCF-7	breast:
2	chr3:101372781..101376576-chr3:101404172..101407222,3	K562	blood:
3	chr3:101361008..101362926-chr3:101370600..101373515,2	K562	blood:

Variant related genes	Relation type
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 93 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs1031710	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1056579	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1138818	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11707250	0.96[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11710533	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11711903	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11712309	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11712748	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11714278	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11714444	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs11717046	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11717638	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11718446	0.81[JPT][hapmap]
rs11720745	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11914318	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11917569	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11919389	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11923273	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11924013	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11925001	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12629658	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633089	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.89[TSI][hapmap]
rs12635128	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636557	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12639028	0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13059470	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13060963	0.86[ASN][1000 genomes]
rs13061565	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13065944	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.85[ASN][1000 genomes]
rs13066768	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.90[ASN][1000 genomes]
rs13077703	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13077925	0.90[ASN][1000 genomes]
rs13081846	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13082236	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs13084113	0.96[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13085776	0.96[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap]
rs13094753	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs13096323	0.81[ASN][1000 genomes]
rs13099674	0.90[ASN][1000 genomes]
rs13100262	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1460097	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap]
rs17345528	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17347156	0.96[CEU][hapmap];0.86[CHB][hapmap]
rs17411983	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2290859	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs2303474	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2318090	0.90[ASN][1000 genomes]
rs3094295	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094296	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3094297	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3109756	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34181125	0.90[ASN][1000 genomes]
rs34301719	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.90[ASN][1000 genomes]
rs34624546	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34883763	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35117343	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.85[MKK][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35850993	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36060163	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3762729	0.95[JPT][hapmap]
rs3804775	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3804778	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs3806653	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3806654	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3864012	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4342086	0.96[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap]
rs55654108	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55859364	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56291106	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59596156	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62282218	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62282255	0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs62284162	0.81[EUR][1000 genomes]
rs62284198	0.90[ASN][1000 genomes]
rs62284199	0.90[ASN][1000 genomes]
rs71625262	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629753	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7645391	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7651721	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9830943	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs997739	0.83[GIH][hapmap];0.95[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13069443	ZBTB11	cis	cerebellum	SCAN
rs13069443	NIT2	cis	parietal	SCAN
rs13069443	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs13069443	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:101362800-101391600	Weak transcription	Stomach Mucosa	stomach
2	chr3:101363000-101381800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:101363400-101382800	Weak transcription	Fetal Heart	heart
6	chr3:101363400-101391400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr3:101364800-101391000	Strong transcription	Primary monocytes fromperipheralblood	blood
8	chr3:101364800-101391000	Strong transcription	Monocytes-CD14+_RO01746	blood
9	chr3:101364800-101392000	Strong transcription	Primary T cells from cord blood	blood
10	chr3:101365000-101378000	Weak transcription	Fetal Brain Male	brain
11	chr3:101365200-101387800	Strong transcription	Liver	Liver
12	chr3:101365400-101385400	Strong transcription	Stomach Smooth Muscle	stomach
13	chr3:101366000-101384800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:101366400-101390400	Strong transcription	Primary T cells fromperipheralblood	blood
15	chr3:101366400-101392200	Strong transcription	Primary B cells from peripheral blood	blood
16	chr3:101366600-101373600	Weak transcription	HSMMtube	muscle
17	chr3:101366600-101380400	Strong transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:101366600-101390800	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr3:101366600-101390800	Strong transcription	Primary neutrophils fromperipheralblood	blood
20	chr3:101366600-101391000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr3:101366600-101391000	Strong transcription	Duodenum Mucosa	Duodenum
22	chr3:101366600-101391000	Strong transcription	Fetal Thymus	thymus
23	chr3:101366600-101391800	Strong transcription	Primary B cells from cord blood	blood
24	chr3:101366800-101374200	Strong transcription	Fetal Brain Female	brain
25	chr3:101366800-101380000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:101366800-101390400	Strong transcription	Fetal Lung	lung
27	chr3:101366800-101391000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:101366800-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
29	chr3:101367000-101374400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr3:101367000-101377000	Strong transcription	HSMM	muscle
31	chr3:101367000-101384600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:101367000-101390800	Strong transcription	Primary T helper cells PMA-I stimulated	--
33	chr3:101367000-101390800	Strong transcription	Dnd41	blood
34	chr3:101367000-101391000	Strong transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:101367000-101391000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
36	chr3:101367000-101391000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr3:101367000-101391000	Strong transcription	Placenta	Placenta
38	chr3:101367000-101391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
39	chr3:101367200-101385400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
40	chr3:101367200-101391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:101367200-101391800	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr3:101367400-101391000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr3:101367400-101391000	Strong transcription	Rectal Mucosa Donor 29	rectum
44	chr3:101367600-101390400	Strong transcription	Skeletal Muscle Female	skeletal muscle
45	chr3:101367800-101380200	Strong transcription	Rectal Mucosa Donor 31	rectum
46	chr3:101367800-101380400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr3:101368000-101378000	Weak transcription	NHLF	lung
48	chr3:101368000-101381600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr3:101368000-101383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr3:101368000-101390600	Strong transcription	Adipose Nuclei	Adipose

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