Variant report

Variant	rs12522956
Chromosome Location	chr5:167741777-167741778
allele	G/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	FOS	chr5:167741684-167742442	MCF10A-Er-Src	breast:	n/a	n/a
2	BCL3	chr5:167741647-167742693	A549	lung:	n/a	chr5:167741867-167741876
3	ARID3A	chr5:167741703-167743613	HepG2	liver:	n/a	n/a
4	REST	chr5:167741622-167742780	A549	lung:	n/a	chr5:167741934-167741954
5	TFAP2C	chr5:167741627-167742349	Hela-S3	cervix:	n/a	n/a
6	MAX	chr5:167741725-167742240	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr5:167741684-167742334	Hela-S3	cervix:	n/a	n/a
8	FOS	chr5:167741686-167742368	MCF10A-Er-Src	breast:	n/a	n/a
9	ELF1	chr5:167741756-167742476	HepG2	liver:	n/a	n/a
10	EP300	chr5:167741767-167742295	Hela-S3	cervix:	n/a	chr5:167742042-167742056 chr5:167742181-167742195
11	STAT3	chr5:167741466-167742473	MCF10A-Er-Src	breast:	n/a	chr5:167741975-167741987 chr5:167742137-167742146 chr5:167742138-167742147
12	MAZ	chr5:167741717-167743135	IMR90	lung:	n/a	chr5:167743063-167743073
13	CEBPB	chr5:167741407-167742260	IMR90	lung:	n/a	n/a
14	TEAD4	chr5:167741564-167742479	SK-N-SH	brain:	n/a	chr5:167741959-167741968
15	POLR2A	chr5:167741693-167743787	HepG2	liver:	n/a	n/a
16	POLR2A	chr5:167741683-167742344	HCT-116	colon:	n/a	n/a
17	GTF2F1	chr5:167741754-167742314	Hela-S3	cervix:	n/a	n/a
18	CEBPB	chr5:167741446-167742251	A549	lung:	n/a	n/a
19	RAD21	chr5:167741644-167742364	ECC-1	luminal epithelium:	n/a	n/a
20	HNF4A	chr5:167741710-167742382	HepG2	liver:	n/a	chr5:167742114-167742129 chr5:167741942-167741957 chr5:167742113-167742128 chr5:167741942-167741957 chr5:167741942-167741957 chr5:167742114-167742129
21	FOSL2	chr5:167741564-167742597	A549	lung:	n/a	n/a
22	FOS	chr5:167741674-167742420	MCF10A-Er-Src	breast:	n/a	n/a
23	PBX3	chr5:167741660-167742456	A549	lung:	n/a	n/a
24	NFIC	chr5:167741664-167742502	SK-N-SH	brain:	n/a	n/a
25	ZEB1	chr5:167741574-167742497	HepG2	liver:	n/a	chr5:167741913-167741920
26	MYC	chr5:167741685-167742397	MCF10A-Er-Src	breast:	n/a	n/a
27	ETS1	chr5:167741741-167742427	A549	lung:	n/a	n/a
28	TEAD4	chr5:167741665-167742590	SK-N-SH	brain:	n/a	chr5:167741959-167741968
29	JUND	chr5:167741681-167742493	SK-N-SH	brain:	n/a	n/a
30	PBX3	chr5:167741617-167742510	SK-N-SH	brain:	n/a	n/a
31	POLR2A	chr5:167741767-167741780	Hela-S3	cervix:	n/a	n/a
32	GABPA	chr5:167741677-167742422	A549	lung:	n/a	n/a
33	POLR2A	chr5:167741690-167741784	A549	lung:	n/a	n/a
34	MAX	chr5:167741499-167742632	A549	lung:	n/a	n/a
35	ZBTB33	chr5:167741724-167742381	A549	lung:	n/a	n/a
36	CREB1	chr5:167741685-167742360	HepG2	liver:	n/a	n/a
37	STAT3	chr5:167741574-167742470	MCF10A-Er-Src	breast:	n/a	chr5:167741975-167741987 chr5:167742137-167742146 chr5:167742138-167742147
38	GATA3	chr5:167741675-167742542	A549	lung:	n/a	n/a
39	ELF1	chr5:167741685-167742450	A549	lung:	n/a	n/a
40	ATF3	chr5:167741670-167742496	A549	lung:	n/a	n/a
41	ZKSCAN1	chr5:167741706-167742277	Hela-S3	cervix:	n/a	n/a
42	PBX3	chr5:167741729-167742458	SK-N-SH	brain:	n/a	n/a
43	CEBPB	chr5:167741600-167742203	HepG2	liver:	n/a	n/a
44	POLR2A	chr5:167741579-167745205	MCF10A-Er-Src	breast:	n/a	n/a
45	NR3C1	chr5:167741687-167742321	A549	lung:	n/a	n/a
46	EP300	chr5:167741571-167742588	A549	lung:	n/a	chr5:167742042-167742056 chr5:167742181-167742195
47	FOSL2	chr5:167741755-167742367	A549	lung:	n/a	n/a
48	MYC	chr5:167741730-167742283	MCF10A-Er-Src	breast:	n/a	n/a
49	RCOR1	chr5:167741685-167742468	Hela-S3	cervix:	n/a	n/a
50	MXI1	chr5:167741661-167742515	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr5:167738439..167740014-chr5:167740372..167743298,2	MCF-7	breast:
2	chr5:167695818..167698583-chr5:167740233..167742676,2	MCF-7	breast:
3	chr5:167741377..167743191-chr5:167790868..167792715,2	MCF-7	breast:
4	chr5:167715928..167721153-chr5:167739241..167745348,16	MCF-7	breast:
5	chr5:167741730..167743301-chr5:167807554..167809969,2	MCF-7	breast:

Variant related genes	Relation type
WWC1	TF binding region
ENSG00000113645	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs12522354	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13183480	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17775705	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17832301	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1966488	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2112556	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2337215	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34509932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35397127	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4331926	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59173424	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs749235	0.90[CHB][hapmap]

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	nsv534607	chr5:167661667-168454396	Active TSS Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
2	nsv949154	chr5:167691208-168323234	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	nsv5119	chr5:167724987-167766076	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:68 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:167727600-167742600	Weak transcription	Fetal Brain Female	brain
2	chr5:167734200-167746000	Enhancers	Fetal Intestine Large	intestine
3	chr5:167734400-167746600	Enhancers	Fetal Intestine Small	intestine
4	chr5:167738200-167742200	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr5:167738200-167747600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr5:167738400-167744400	Weak transcription	Brain Inferior Temporal Lobe	brain
7	chr5:167738600-167741800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr5:167739400-167741800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr5:167739400-167742800	Enhancers	Muscle Satellite Cultured Cells	--
10	chr5:167739400-167745000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr5:167739600-167743600	Enhancers	HSMM	muscle
12	chr5:167739600-167745000	Enhancers	Pancreas	Pancrea
13	chr5:167739800-167742000	Weak transcription	HSMMtube	muscle
14	chr5:167739800-167745200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr5:167740000-167742800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr5:167740200-167742800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr5:167740200-167743000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr5:167740200-167744400	Weak transcription	Right Atrium	heart
19	chr5:167740200-167744800	Enhancers	Breast Myoepithelial Primary Cells	Breast
20	chr5:167740200-167745600	Enhancers	NH-A	brain
21	chr5:167740400-167742000	Weak transcription	Brain Hippocampus Middle	brain
22	chr5:167740600-167742400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr5:167740600-167742600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr5:167740800-167741800	Enhancers	Sigmoid Colon	Sigmoid Colon
25	chr5:167740800-167744600	Enhancers	Esophagus	oesophagus
26	chr5:167740800-167744800	Enhancers	H1 Cell Line	embryonic stem cell
27	chr5:167740800-167744800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr5:167740800-167745200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr5:167740800-167745200	Enhancers	Stomach Mucosa	stomach
30	chr5:167740800-167745200	Enhancers	HMEC	breast
31	chr5:167740800-167745600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr5:167740800-167745600	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr5:167740800-167747000	Enhancers	Placenta	Placenta
34	chr5:167741000-167742600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr5:167741000-167742600	Enhancers	Brain Cingulate Gyrus	brain
36	chr5:167741000-167743200	Enhancers	Colonic Mucosa	Colon
37	chr5:167741000-167743400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
38	chr5:167741000-167744600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr5:167741000-167744600	Enhancers	Lung	lung
40	chr5:167741000-167745000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr5:167741000-167745000	Enhancers	NHDF-Ad	bronchial
42	chr5:167741000-167745200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
43	chr5:167741000-167745200	Enhancers	NHLF	lung
44	chr5:167741200-167741800	Weak transcription	Brain Anterior Caudate	brain
45	chr5:167741200-167742200	Enhancers	Duodenum Mucosa	Duodenum
46	chr5:167741600-167741800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
47	chr5:167741600-167741800	Enhancers	Gastric	stomach
48	chr5:167741600-167742000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr5:167741600-167742000	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
50	chr5:167741600-167742000	Flanking Active TSS	Liver	Liver

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