Variant report

Variant	rs11712748
Chromosome Location	chr3:101383562-101383563
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:101381844..101383869-chr3:101386784..101389655,2	MCF-7	breast:
2	chr3:101382560..101384971-chr3:101397220..101399534,3	MCF-7	breast:
3	chr3:101382840..101386028-chr3:101403926..101406751,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114391	Chromatin interaction

Extended variants
information (count: 94 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:93)

rs_ID	r²[population]
rs1031710	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1056579	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1138818	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11706986	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11707250	0.92[CEU][hapmap];0.86[CHB][hapmap];0.84[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs11710533	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11710805	0.84[ASN][1000 genomes]
rs11711079	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11711903	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs11712309	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11714278	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714444	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs11717046	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11717638	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs11718446	0.81[JPT][hapmap]
rs11720745	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11914318	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11917569	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11917682	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11919389	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11923273	0.81[AMR][1000 genomes]
rs11924013	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11925001	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12629658	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12629954	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12633089	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs12635128	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12636557	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12639028	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13059470	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13060963	0.87[ASN][1000 genomes]
rs13061565	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13065944	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.86[ASN][1000 genomes]
rs13066768	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs13068350	0.81[ASN][1000 genomes]
rs13069443	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]
rs13077703	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13077925	0.91[ASN][1000 genomes]
rs13081846	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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13082236	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13084113	0.92[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap]
rs13085776	0.92[CEU][hapmap];0.85[CHB][hapmap];0.81[JPT][hapmap]
rs13094753	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs13096323	0.82[ASN][1000 genomes]
rs13099674	0.91[ASN][1000 genomes]
rs13100262	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1460097	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap]
rs17345528	0.83[GIH][hapmap];0.95[JPT][hapmap]
rs17347156	0.92[CEU][hapmap];0.86[CHB][hapmap]
rs17411983	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1963961	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1963962	0.91[ASN][1000 genomes]
rs2288272	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];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2290859	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.92[TSI][hapmap]
rs2303474	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2318090	0.91[ASN][1000 genomes]
rs3094295	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094296	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3094297	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];0.90[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3109756	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34181125	0.91[ASN][1000 genomes]
rs34301719	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34376498	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.92[TSI][hapmap];0.91[ASN][1000 genomes]
rs34624546	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34883763	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35117343	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35850993	0.81[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.92[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36002990	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36060163	0.93[AMR][1000 genomes];0.96[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	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];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3806654	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3864012	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4342086	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];0.90[GIH][hapmap];0.92[TSI][hapmap]
rs55654108	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55821257	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55859364	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56291106	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59596156	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282218	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62282255	0.81[ASN][1000 genomes]
rs62284162	0.83[EUR][1000 genomes]
rs62284198	0.91[ASN][1000 genomes]
rs62284199	0.91[ASN][1000 genomes]
rs71625262	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7629753	0.93[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];0.98[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7645391	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7651406	0.94[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7651721	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];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9830943	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[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
rs11712748	ZBTB11	cis	cerebellum	SCAN
rs11712748	RP11-49I4.3	cis	Esophagus Muscularis	GTEx
rs11712748	NIT2	cis	parietal	SCAN
rs11712748	NXPE3	cis	Esophagus Muscularis	GTEx

Chromatin state (count:124 , 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	chr3:101363000-101394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:101363200-101394400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr3:101363400-101391400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr3:101364800-101391000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr3:101364800-101391000	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr3:101364800-101392000	Strong transcription	Primary T cells from cord blood	blood
8	chr3:101365200-101387800	Strong transcription	Liver	Liver
9	chr3:101365400-101385400	Strong transcription	Stomach Smooth Muscle	stomach
10	chr3:101366000-101384800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr3:101366400-101390400	Strong transcription	Primary T cells fromperipheralblood	blood
12	chr3:101366400-101392200	Strong transcription	Primary B cells from peripheral blood	blood
13	chr3:101366600-101390800	Strong transcription	HUES6 Cell Line	embryonic stem cell
14	chr3:101366600-101390800	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr3:101366600-101391000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
16	chr3:101366600-101391000	Strong transcription	Duodenum Mucosa	Duodenum
17	chr3:101366600-101391000	Strong transcription	Fetal Thymus	thymus
18	chr3:101366600-101391800	Strong transcription	Primary B cells from cord blood	blood
19	chr3:101366800-101390400	Strong transcription	Fetal Lung	lung
20	chr3:101366800-101391000	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
21	chr3:101366800-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr3:101367000-101384600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr3:101367000-101390800	Strong transcription	Primary T helper cells PMA-I stimulated	--
24	chr3:101367000-101390800	Strong transcription	Dnd41	blood
25	chr3:101367000-101391000	Strong transcription	HUES64 Cell Line	embryonic stem cell
26	chr3:101367000-101391000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr3:101367000-101391000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
28	chr3:101367000-101391000	Strong transcription	Placenta	Placenta
29	chr3:101367000-101391400	Strong transcription	Primary T helper cells fromperipheralblood	blood
30	chr3:101367200-101385400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
31	chr3:101367200-101391000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr3:101367200-101391800	Strong transcription	HUES48 Cell Line	embryonic stem cell
33	chr3:101367400-101391000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr3:101367400-101391000	Strong transcription	Rectal Mucosa Donor 29	rectum
35	chr3:101367600-101390400	Strong transcription	Skeletal Muscle Female	skeletal muscle
36	chr3:101368000-101383800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr3:101368000-101390600	Strong transcription	Adipose Nuclei	Adipose
38	chr3:101368000-101391000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr3:101368000-101391600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr3:101368200-101391000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr3:101368400-101390400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:101368400-101391000	Strong transcription	Primary hematopoietic stem cells	blood
43	chr3:101369000-101390800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
44	chr3:101369400-101391000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr3:101369600-101384600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:101369600-101388200	Strong transcription	Brain Anterior Caudate	brain
47	chr3:101369800-101384600	Strong transcription	H1 Cell Line	embryonic stem cell
48	chr3:101369800-101385400	Strong transcription	Sigmoid Colon	Sigmoid Colon
49	chr3:101369800-101385800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr3:101369800-101387400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood

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