Variant report

Variant	rs12912258
Chromosome Location	chr15:74494388-74494389
allele	C/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	CHD2	chr15:74492673-74494429	Hela-S3	cervix:	n/a	n/a
2	SMARCB1	chr15:74492604-74494571	Hela-S3	cervix:	n/a	n/a
3	TFAP2C	chr15:74492581-74495035	Hela-S3	cervix:	n/a	chr15:74493490-74493505 chr15:74492911-74492926
4	CEBPB	chr15:74492569-74494496	Hela-S3	cervix:	n/a	n/a
5	SMARCC1	chr15:74492611-74495990	Hela-S3	cervix:	n/a	n/a
6	ZNF143	chr15:74494025-74494505	Hela-S3	cervix:	n/a	n/a
7	RCOR1	chr15:74492582-74494497	Hela-S3	cervix:	n/a	n/a
8	FOS	chr15:74494030-74494391	MCF10A-Er-Src	breast:	n/a	n/a
9	TCF7L2	chr15:74494239-74495419	HEK293	kidney:	n/a	chr15:74495085-74495099 chr15:74495087-74495096 chr15:74494949-74494956
10	FOSL2	chr15:74493948-74494465	A549	lung:	n/a	n/a
11	GTF2F1	chr15:74492627-74494466	Hela-S3	cervix:	n/a	n/a
12	ZNF263	chr15:74493214-74494496	HEK293-T-REx	kidney:	n/a	n/a
13	SIN3AK20	chr15:74492465-74494667	MCF-7	breast:	n/a	n/a
14	SMC3	chr15:74492634-74494453	Hela-S3	cervix:	n/a	n/a
15	FOS	chr15:74493980-74494432	MCF10A-Er-Src	breast:	n/a	n/a
16	RAD21	chr15:74492648-74494437	Hela-S3	cervix:	n/a	n/a
17	EP300	chr15:74494016-74494452	Hela-S3	cervix:	n/a	n/a
18	TFAP2A	chr15:74492626-74495193	Hela-S3	cervix:	n/a	chr15:74494897-74494905 chr15:74494886-74494898 chr15:74494905-74494916 chr15:74494897-74494905 chr15:74495170-74495180 chr15:74494896-74494904 chr15:74494897-74494905 chr15:74493490-74493505 chr15:74494896-74494904 chr15:74493234-74493249 chr15:74494896-74494904 chr15:74494886-74494898

No.	Distal block	Cell Line	Cell type
1	chr15:74478980..74480513-chr15:74491993..74494403,2	MCF-7	breast:
2	chr15:74492912..74495035-chr15:74502031..74504562,2	MCF-7	breast:
3	chr15:74481853..74488513-chr15:74489689..74497281,13	MCF-7	breast:
4	chr15:74421502..74423343-chr15:74491775..74494417,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000259264	TF binding region
ENSG00000167178	Chromatin interaction
ENSG00000248540	Chromatin interaction
ENSG00000137868	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs11630317	0.82[CEU][hapmap];0.85[EUR][1000 genomes]
rs11630924	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11631509	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11631944	0.82[CEU][hapmap];0.81[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs11633687	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11639090	0.88[EUR][1000 genomes]
rs11639369	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11854957	0.85[CEU][hapmap];0.88[EUR][1000 genomes]
rs11857410	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12899173	0.82[CEU][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12905521	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12907503	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12911581	0.81[CEU][hapmap];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12912578	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.89[EUR][1000 genomes]
rs12913041	0.89[EUR][1000 genomes]
rs12915891	0.91[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13259	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs2062309	0.86[EUR][1000 genomes]
rs2415169	0.88[EUR][1000 genomes]
rs2899824	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs34004794	0.81[AMR][1000 genomes]
rs34147822	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34234753	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34573746	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34591452	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34868798	0.88[EUR][1000 genomes]
rs34985083	0.81[AMR][1000 genomes]
rs35036456	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs35255788	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35462746	0.87[EUR][1000 genomes]
rs35661273	0.88[EUR][1000 genomes]
rs35917667	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3848160	0.88[EUR][1000 genomes]
rs3848161	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs3888004	0.82[CEU][hapmap];0.82[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs409856	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs62003660	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62003661	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005707	0.88[EUR][1000 genomes]
rs62005709	0.88[EUR][1000 genomes]
rs62005710	0.88[EUR][1000 genomes]
rs62005711	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs71399778	0.88[EUR][1000 genomes]
rs7169600	1.00[YRI][hapmap]
rs72747610	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs733163	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs8037531	0.87[EUR][1000 genomes]
rs923118	0.82[GIH][hapmap];0.86[TSI][hapmap];0.88[EUR][1000 genomes]
rs9630417	0.82[GIH][hapmap];0.86[TSI][hapmap];0.86[EUR][1000 genomes]
rs971755	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971756	1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs971757	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv833053	chr15:74360156-74555140	Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv833054	chr15:74457643-74625283	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	nsv904345	chr15:74458181-74526596	Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv904346	chr15:74458181-74548773	Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv904347	chr15:74462629-74537101	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv904348	chr15:74462629-74542686	Genic enhancers Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	nsv471253	chr15:74489207-74545148	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74489200-74509600	Weak transcription	Gastric	stomach
2	chr15:74489400-74499000	Weak transcription	Brain Anterior Caudate	brain
3	chr15:74490600-74496200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
4	chr15:74491000-74503200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:74491400-74494800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr15:74492000-74496800	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr15:74492400-74495000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
8	chr15:74492600-74494400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr15:74492600-74494600	Enhancers	Esophagus	oesophagus
10	chr15:74492600-74494600	Enhancers	Spleen	Spleen
11	chr15:74492600-74494800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:74492600-74494800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:74492600-74494800	Flanking Active TSS	A549	lung
14	chr15:74492600-74494800	Enhancers	NHEK	skin
15	chr15:74492600-74495000	Enhancers	Right Atrium	heart
16	chr15:74492600-74495000	Enhancers	NHDF-Ad	bronchial
17	chr15:74492600-74495400	Flanking Active TSS	Placenta	Placenta
18	chr15:74492600-74495400	Enhancers	Right Ventricle	heart
19	chr15:74492600-74495600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:74492600-74495800	Flanking Active TSS	Hela-S3	cervix
21	chr15:74492600-74496200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:74492600-74496400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr15:74492600-74496400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr15:74492600-74496600	Enhancers	HMEC	breast
25	chr15:74492600-74496800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr15:74492600-74497000	Enhancers	Ovary	ovary
27	chr15:74492600-74497000	Enhancers	Placenta Amnion	Placenta Amnion
28	chr15:74492600-74497400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:74492600-74497800	Enhancers	GM12878-XiMat	blood
30	chr15:74492600-74498000	Enhancers	Fetal Lung	lung
31	chr15:74492600-74503200	Enhancers	Fetal Muscle Leg	muscle
32	chr15:74492800-74494400	Enhancers	ES-I3 Cell Line	embryonic stem cell
33	chr15:74492800-74494400	Enhancers	NHLF	lung
34	chr15:74492800-74494600	Enhancers	HSMMtube	muscle
35	chr15:74492800-74494800	Enhancers	Fetal Kidney	kidney
36	chr15:74492800-74494800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr15:74492800-74496600	Enhancers	Fetal Heart	heart
38	chr15:74493000-74494800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
39	chr15:74493000-74495000	Enhancers	Fetal Thymus	thymus
40	chr15:74493000-74496800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
41	chr15:74493200-74494400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:74493200-74494600	Bivalent Enhancer	H1 Cell Line	embryonic stem cell
43	chr15:74493200-74494600	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
44	chr15:74493200-74494800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr15:74493200-74494800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:74493200-74496800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:74493400-74494400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
48	chr15:74493400-74494600	Enhancers	Fetal Intestine Small	intestine
49	chr15:74493400-74494800	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:74493400-74494800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin

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