Variant report

Variant	rs3762797
Chromosome Location	chr3:28381887-28381888
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:28381841-28381989	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr3:28381770-28381970	MCF10A-Er-Src	breast:	n/a	chr3:28381776-28381790

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:28378547..28380122-chr3:28381729..28384245,2	MCF-7	breast:

Variant related genes	Relation type
AZI2	TF binding region
ENSG00000163512	Chromatin interaction

Extended variants
information (count: 124 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs1037723	0.92[ASN][1000 genomes]
rs11705962	0.88[ASN][1000 genomes]
rs11706332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11707705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11710963	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11712484	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11712489	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11720107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11918050	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11921692	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11921943	1.00[CHB][hapmap]
rs11924173	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11926399	0.95[ASN][1000 genomes]
rs12107256	0.85[CHB][hapmap]
rs13066118	0.86[ASN][1000 genomes]
rs13069839	0.80[ASN][1000 genomes]
rs13074633	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13075840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs13080155	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs13081520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13081787	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13082167	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs13083544	0.85[CHB][hapmap]
rs13085075	1.00[CHB][hapmap]
rs13087143	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13087774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13088574	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13090296	0.85[CHB][hapmap]
rs13090439	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13093242	0.85[CHB][hapmap]
rs13095628	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13095675	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs13099152	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1457909	0.89[ASN][1000 genomes]
rs1457910	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1585211	1.00[CHB][hapmap]
rs1598846	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1599826	0.92[CHB][hapmap]
rs1606386	0.88[CEU][hapmap];0.93[CHB][hapmap];0.89[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1606388	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1610238	0.85[CHB][hapmap]
rs17021221	0.85[CHB][hapmap]
rs17021306	0.85[CHB][hapmap]
rs17021402	0.96[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17357206	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17638742	0.91[CEU][hapmap];0.92[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17638782	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17638991	0.95[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17639978	0.95[CEU][hapmap]
rs17695765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17695884	0.96[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17696025	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17696459	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17696561	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17696783	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs1870259	1.00[CHB][hapmap]
rs1975828	0.80[ASN][1000 genomes]
rs1975829	0.81[ASN][1000 genomes]
rs2168799	1.00[CHB][hapmap]
rs34311197	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34574968	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34796684	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35088087	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35137555	0.89[ASN][1000 genomes]
rs35177150	0.92[ASN][1000 genomes]
rs35702956	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35736614	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35825908	0.92[ASN][1000 genomes]
rs35845822	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs36051688	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs36105900	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4234337	0.87[ASN][1000 genomes]
rs4256085	0.87[ASN][1000 genomes]
rs4295137	0.87[ASN][1000 genomes]
rs4322963	0.87[ASN][1000 genomes]
rs4428136	0.86[ASN][1000 genomes]
rs4450765	0.87[ASN][1000 genomes]
rs4452283	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4522735	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4680750	0.80[ASN][1000 genomes]
rs4680753	0.87[ASN][1000 genomes]
rs4680909	1.00[CHB][hapmap]
rs4680913	1.00[CHB][hapmap]
rs58918848	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs59975750	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60043893	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62250271	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62250272	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62250273	0.93[ASN][1000 genomes]
rs62250296	0.92[ASN][1000 genomes]
rs62251105	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62251108	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62251131	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62251134	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62251138	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62251144	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62252069	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6551255	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66502736	0.80[ASN][1000 genomes]
rs66733194	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66767946	0.88[ASN][1000 genomes]
rs6763313	0.80[ASN][1000 genomes]
rs6771057	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs6771460	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6803692	1.00[CHB][hapmap]
rs68085718	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71087683	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7434193	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7627471	0.86[ASN][1000 genomes]
rs7627575	0.87[ASN][1000 genomes]
rs7635383	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7638450	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7639750	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7641491	1.00[CHB][hapmap]
rs7643191	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7649498	1.00[CHB][hapmap];0.80[ASN][1000 genomes]
rs7650831	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7651883	1.00[CHB][hapmap]
rs952888	0.86[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9683360	0.92[ASN][1000 genomes]
rs969443	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs9843464	1.00[CHB][hapmap];0.80[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	esv3328565	chr3:27991169-28915035	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
2	nsv876649	chr3:28126595-28718454	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
2	chr3:28343800-28383800	Weak transcription	Aorta	Aorta
3	chr3:28349800-28389400	Weak transcription	Gastric	stomach
4	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
5	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr3:28360400-28383800	Weak transcription	Rectal Smooth Muscle	rectum
7	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr3:28361600-28382200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:28362800-28382400	Strong transcription	Primary neutrophils fromperipheralblood	blood
10	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
11	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
13	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
14	chr3:28364800-28382400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
15	chr3:28365400-28383800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr3:28365400-28389400	Weak transcription	Lung	lung
17	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
19	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
20	chr3:28367000-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
22	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr3:28367200-28384000	Weak transcription	Fetal Heart	heart
24	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
25	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
27	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr3:28368400-28387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr3:28368400-28388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr3:28369000-28382000	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr3:28369000-28382400	Strong transcription	Primary monocytes fromperipheralblood	blood
32	chr3:28369600-28382200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
33	chr3:28370200-28384000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
34	chr3:28370600-28383400	Weak transcription	Colon Smooth Muscle	Colon
35	chr3:28371800-28383000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr3:28372200-28382000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr3:28372400-28382000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:28372400-28384200	Weak transcription	A549	lung
39	chr3:28372400-28388400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr3:28372800-28382400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr3:28373200-28382800	Weak transcription	NHLF	lung
42	chr3:28373400-28388400	Weak transcription	Stomach Mucosa	stomach
43	chr3:28374000-28387800	Weak transcription	Brain Germinal Matrix	brain
44	chr3:28375400-28383600	Weak transcription	Fetal Stomach	stomach
45	chr3:28376600-28382000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:28376600-28382600	Strong transcription	Hela-S3	cervix
47	chr3:28376800-28382000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr3:28376800-28382000	Strong transcription	Liver	Liver
49	chr3:28377000-28382000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr3:28377000-28382000	Strong transcription	Osteobl	bone

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