Variant report

Variant	rs12054402
Chromosome Location	chr3:28384051-28384052
allele	A/G
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	STAT3	chr3:28383762-28384290	MCF10A-Er-Src	breast:	n/a	chr3:28383936-28383959
2	POLR2A	chr3:28383824-28384342	MCF10A-Er-Src	breast:	n/a	n/a
3	ESR1	chr3:28383814-28384378	ECC-1	luminal epithelium:	n/a	n/a
4	STAT3	chr3:28383755-28384251	MCF10A-Er-Src	breast:	n/a	chr3:28383936-28383959
5	ARID3A	chr3:28383803-28384263	K562	blood:	n/a	n/a
6	FOS	chr3:28383811-28384249	MCF10A-Er-Src	breast:	n/a	chr3:28383953-28383960 chr3:28384113-28384122
7	CEBPB	chr3:28383769-28384255	IMR90	lung:	n/a	n/a
8	ESR1	chr3:28383876-28384425	ECC-1	luminal epithelium:	n/a	n/a
9	ZNF143	chr3:28383910-28384331	GM12878	blood:	n/a	n/a
10	MYC	chr3:28383913-28384257	MCF10A-Er-Src	breast:	n/a	chr3:28383965-28383974
11	MYC	chr3:28383949-28384287	MCF10A-Er-Src	breast:	n/a	chr3:28383965-28383974
12	FOS	chr3:28383789-28384349	MCF10A-Er-Src	breast:	n/a	chr3:28383953-28383960 chr3:28384113-28384122
13	ZNF143	chr3:28383983-28384183	Hela-S3	cervix:	n/a	n/a
14	FOS	chr3:28383780-28384264	MCF10A-Er-Src	breast:	n/a	chr3:28383953-28383960 chr3:28384113-28384122
15	E2F4	chr3:28383820-28384264	MCF10A-Er-Src	breast:	n/a	n/a
16	FOS	chr3:28383800-28384230	MCF10A-Er-Src	breast:	n/a	chr3:28383953-28383960 chr3:28384113-28384122
17	POLR2A	chr3:28383802-28384109	MCF10A-Er-Src	breast:	n/a	n/a
18	STAT3	chr3:28383746-28384254	MCF10A-Er-Src	breast:	n/a	chr3:28383936-28383959
19	STAT3	chr3:28383765-28384265	MCF10A-Er-Src	breast:	n/a	chr3:28383936-28383959

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: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10510607	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs10510609	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs13100556	0.84[GIH][hapmap]
rs17021298	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs1845166	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs2125204	0.93[GIH][hapmap];0.82[MEX][hapmap];1.00[MKK][hapmap]
rs4502545	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs4680748	0.82[CHB][hapmap]
rs4680751	0.84[GIH][hapmap]
rs4680906	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap];0.81[ASN][1000 genomes]
rs55954817	0.82[ASN][1000 genomes]
rs56116734	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6764496	0.95[CHB][hapmap];0.88[JPT][hapmap]
rs6781639	0.84[GIH][hapmap]
rs6805743	0.84[GIH][hapmap]
rs7645825	0.86[JPT][hapmap]

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:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:28317600-28389400	Weak transcription	Esophagus	oesophagus
2	chr3:28349800-28389400	Weak transcription	Gastric	stomach
3	chr3:28358600-28386400	Weak transcription	Thymus	Thymus
4	chr3:28358800-28389000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:28360400-28387400	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr3:28362800-28387800	Weak transcription	HUVEC	blood vessel
7	chr3:28363600-28389000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:28363800-28389600	Weak transcription	Spleen	Spleen
9	chr3:28364000-28388400	Weak transcription	Fetal Brain Female	brain
10	chr3:28365400-28389400	Weak transcription	Lung	lung
11	chr3:28366000-28388600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr3:28366200-28389400	Weak transcription	Colonic Mucosa	Colon
13	chr3:28366400-28389200	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr3:28367000-28384200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr3:28367000-28388800	Weak transcription	Brain Angular Gyrus	brain
16	chr3:28367000-28389000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
17	chr3:28367200-28387800	Weak transcription	Fetal Brain Male	brain
18	chr3:28367200-28388800	Weak transcription	Brain Cingulate Gyrus	brain
19	chr3:28367200-28389400	Weak transcription	Pancreas	Pancrea
20	chr3:28367400-28388800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr3:28368400-28387600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr3:28368400-28388800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr3:28372400-28384200	Weak transcription	A549	lung
24	chr3:28372400-28388400	Weak transcription	Primary hematopoietic stem cells	blood
25	chr3:28373400-28388400	Weak transcription	Stomach Mucosa	stomach
26	chr3:28374000-28387800	Weak transcription	Brain Germinal Matrix	brain
27	chr3:28377200-28384400	Weak transcription	Small Intestine	intestine
28	chr3:28377800-28387600	Weak transcription	Cortex derived primary cultured neurospheres	brain
29	chr3:28377800-28387600	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr3:28377800-28388600	Weak transcription	Brain Substantia Nigra	brain
31	chr3:28377800-28389200	Weak transcription	Primary B cells from peripheral blood	blood
32	chr3:28378400-28389400	Weak transcription	Ovary	ovary
33	chr3:28378800-28384200	Weak transcription	Fetal Intestine Small	intestine
34	chr3:28378800-28387400	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:28379000-28389600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
36	chr3:28379200-28386400	Weak transcription	Brain Anterior Caudate	brain
37	chr3:28379200-28387800	Weak transcription	Psoas Muscle	Psoas
38	chr3:28379200-28388200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr3:28379400-28384600	Weak transcription	Primary T cells from cord blood	blood
40	chr3:28379400-28388800	Weak transcription	Fetal Muscle Leg	muscle
41	chr3:28379600-28386400	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr3:28379600-28387800	Weak transcription	Primary B cells from cord blood	blood
43	chr3:28380200-28384400	Weak transcription	K562	blood
44	chr3:28380200-28387600	Weak transcription	Rectal Mucosa Donor 29	rectum
45	chr3:28380600-28384200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr3:28380600-28388400	Weak transcription	Fetal Intestine Large	intestine
47	chr3:28380600-28388400	Weak transcription	HSMMtube	muscle
48	chr3:28380600-28389200	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr3:28380800-28384400	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr3:28380800-28384600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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