Variant report

Variant	rs12906973
Chromosome Location	chr15:93254608-93254609
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	chr15:93254327-93255416	H1-hESC	embryonic stem cell:	n/a	n/a
2	E2F6	chr15:93254581-93255162	H1-hESC	embryonic stem cell:	n/a	chr15:93255025-93255034 chr15:93255022-93255034 chr15:93254936-93254948
3	RAD21	chr15:93254606-93255158	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93252649..93254753-chr15:93257319..93260184,2	MCF-7	breast:
2	chr15:93250790..93254703-chr15:93255991..93258300,4	MCF-7	breast:

Variant related genes	Relation type
HMGN1P38	TF binding region

Extended variants
information (count: 53 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1004309	0.94[ASN][1000 genomes]
rs12439654	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12440201	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12440617	0.90[ASN][1000 genomes]
rs12442362	0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12442555	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1561304	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17648050	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1808818	0.91[ASN][1000 genomes]
rs2278519	0.88[ASN][1000 genomes]
rs2278520	0.94[ASN][1000 genomes]
rs2278521	0.94[ASN][1000 genomes]
rs2387911	0.83[ASN][1000 genomes]
rs34188575	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34327113	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs34913881	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35017636	0.80[AMR][1000 genomes]
rs35095971	0.98[ASN][1000 genomes]
rs35277112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35351684	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35663415	0.99[ASN][1000 genomes]
rs35839849	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35982819	0.99[ASN][1000 genomes]
rs35984805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4777729	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4777730	0.92[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4777731	0.92[ASN][1000 genomes]
rs4778033	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs58894958	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs66824972	0.89[ASN][1000 genomes]
rs66934257	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs67759391	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs67770259	0.98[ASN][1000 genomes]
rs71412559	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs71412560	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71412561	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71412562	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs71412563	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71412564	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71412566	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71412567	0.95[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71412568	0.87[EUR][1000 genomes]
rs71412570	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs71412571	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs7165223	0.87[ASN][1000 genomes]
rs7183236	0.98[ASN][1000 genomes]
rs8039425	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1037972	chr15:92804908-93270761	Flanking Bivalent TSS/Enh Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
3	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS 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	169 gene(s)	inside rSNPs	diseases
4	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
5	nsv1040501	chr15:93177153-93286393	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
6	nsv974620	chr15:93252874-93258773	Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93245600-93257400	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr15:93246200-93257400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:93249400-93257400	Weak transcription	Brain Substantia Nigra	brain
4	chr15:93249600-93257200	Weak transcription	Brain Anterior Caudate	brain
5	chr15:93250200-93257200	Weak transcription	Brain Inferior Temporal Lobe	brain
6	chr15:93253200-93257200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr15:93253200-93257200	Weak transcription	HUVEC	blood vessel
8	chr15:93253400-93256600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr15:93253400-93257200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:93254200-93255200	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
11	chr15:93254400-93255000	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr15:93254600-93254800	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr15:93254600-93255000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:93254600-93255000	Flanking Active TSS	Placenta	Placenta
15	chr15:93254600-93255200	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell

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