Variant report

Variant	rs12907503
Chromosome Location	chr15:74479539-74479540
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	POLR2A	chr15:74479212-74480270	A549	lung:	n/a	n/a
2	GATA3	chr15:74479496-74480089	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:74477830..74479940-chr15:74481480..74483032,2	MCF-7	breast:
2	chr15:74478980..74480513-chr15:74491993..74494403,2	MCF-7	breast:
3	chr15:74476268..74481114-chr15:74481144..74486021,6	MCF-7	breast:
4	chr15:74468916..74471772-chr15:74477049..74479874,2	MCF-7	breast:

Variant related genes	Relation type
STRA6	TF binding region
ENSG00000137868	Chromatin interaction
ENSG00000261543	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11630317	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11630924	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11631509	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11631944	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11639090	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11639369	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11854957	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11855667	0.83[EUR][1000 genomes]
rs11857410	0.91[EUR][1000 genomes]
rs12899173	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12911581	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12912258	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12912578	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12913041	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12915891	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13259	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2062309	0.93[EUR][1000 genomes]
rs2415169	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2899824	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34147822	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs34573746	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34868798	0.95[EUR][1000 genomes]
rs351242	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs35255788	0.91[EUR][1000 genomes]
rs35462746	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35661273	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3848160	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3848161	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3888004	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs409856	1.00[CEU][hapmap];0.99[EUR][1000 genomes]
rs62003660	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs62003661	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62005707	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs62005709	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62005710	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62005711	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71399778	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs733163	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs8037531	0.94[EUR][1000 genomes]
rs923118	0.95[EUR][1000 genomes]
rs9630417	0.93[EUR][1000 genomes]
rs971755	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs971756	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs971757	0.83[AMR][1000 genomes];0.92[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	nsv1050884	chr15:74394983-74489413	Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	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
4	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
5	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
6	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
7	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

No data

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74466200-74492800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:74466600-74480600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:74469200-74491800	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr15:74469400-74487600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:74469400-74493200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:74470600-74484000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr15:74470800-74492800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:74473600-74488200	Weak transcription	Right Atrium	heart
9	chr15:74474000-74483400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:74474600-74487200	Weak transcription	Fetal Intestine Small	intestine
11	chr15:74475200-74480000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:74475600-74483000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:74476400-74482600	Weak transcription	A549	lung
14	chr15:74477000-74479800	Enhancers	GM12878-XiMat	blood
15	chr15:74477400-74481400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:74478000-74481000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:74478200-74482600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr15:74478600-74483800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
19	chr15:74478600-74484000	Weak transcription	HSMM	muscle
20	chr15:74478600-74484000	Weak transcription	NHDF-Ad	bronchial
21	chr15:74478600-74485000	Weak transcription	Esophagus	oesophagus
22	chr15:74478600-74491400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:74478800-74484000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr15:74479400-74479800	Genic enhancers	Placenta	Placenta
25	chr15:74479400-74482000	Strong transcription	Fetal Stomach	stomach
26	chr15:74479400-74485000	Weak transcription	NH-A	brain

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