Variant report

Variant	rs2304823
Chromosome Location	chr15:78474476-78474477
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	CTCF	chr15:78474460-78474610	SK-N-SH_RA	brain:	n/a	n/a
2	MAX	chr15:78474442-78474498	HepG2	liver:	n/a	n/a
3	USF1	chr15:78474370-78474545	K562	blood:	n/a	chr15:78474477-78474488
4	YY1	chr15:78474262-78474490	K562	blood:	n/a	n/a
5	CTCF	chr15:78474340-78474490	HepG2	liver:	n/a	n/a
6	CTCF	chr15:78474422-78474659	K562	blood:	n/a	n/a
7	MAX	chr15:78474278-78474612	K562	blood:	n/a	n/a
8	USF2	chr15:78474365-78474522	HepG2	liver:	n/a	n/a
9	USF1	chr15:78474327-78474621	HepG2	liver:	n/a	chr15:78474477-78474488
10	BHLHE40	chr15:78474298-78474571	K562	blood:	n/a	n/a
11	CTCF	chr15:78474407-78474528	H1-hESC	embryonic stem cell:	n/a	n/a
12	GABPA	chr15:78474333-78474621	K562	blood:	n/a	n/a
13	USF1	chr15:78474310-78474653	K562	blood:	n/a	chr15:78474477-78474488
14	CTCF	chr15:78474319-78474694	K562	blood:	n/a	n/a
15	CTCF	chr15:78474438-78474500	GM10248	blood:	n/a	n/a
16	CTCF	chr15:78474341-78474585	K562	blood:	n/a	n/a
17	CTCF	chr15:78474380-78474530	WERI-Rb-1	eye:	n/a	n/a
18	CTCF	chr15:78474380-78474530	MCF-7	breast:	n/a	n/a
19	CTCF	chr15:78474340-78474490	Hela-S3	cervix:	n/a	n/a
20	CTCF	chr15:78474394-78474531	K562	blood:	n/a	n/a
21	YY1	chr15:78474293-78474577	HepG2	liver:	n/a	n/a
22	CTCF	chr15:78474410-78474533	MCF-7	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:78474102..78476021-chr7:20368529..20371433,2	MCF-7	breast:

Variant related genes	Relation type
ACSBG1	TF binding region
ENSG00000271133	Chromatin interaction
ENSG00000105855	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11072732	0.89[MEX][hapmap]
rs11852636	0.94[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12439537	1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs12442037	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs16969507	1.00[CEU][hapmap]
rs16969508	1.00[CEU][hapmap]
rs16969548	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[TSI][hapmap];1.00[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2018983	0.94[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs2271901	1.00[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2304825	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs3784328	1.00[CEU][hapmap]
rs3816253	0.85[CHB][hapmap];0.92[JPT][hapmap]
rs56803002	1.00[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs59824250	0.98[ASN][1000 genomes]
rs7359294	1.00[CEU][hapmap]
rs74024174	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]

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	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv948437	chr15:78435527-78504662	Strong transcription Bivalent Enhancer Weak transcription ZNF genes & repeats Genic enhancers Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv904430	chr15:78466127-78507316	Enhancers Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78447000-78475200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr15:78464800-78475000	Weak transcription	HMEC	breast
3	chr15:78465200-78475000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr15:78465200-78475600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
5	chr15:78465400-78474800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
6	chr15:78465400-78475200	Weak transcription	NHEK	skin
7	chr15:78467200-78477200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:78467400-78474800	Weak transcription	Fetal Brain Female	brain
9	chr15:78467400-78475400	Enhancers	Fetal Thymus	thymus
10	chr15:78470200-78477000	Weak transcription	Brain Cingulate Gyrus	brain
11	chr15:78470200-78486600	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:78470400-78493800	Weak transcription	Brain Substantia Nigra	brain
13	chr15:78470600-78477200	Weak transcription	Brain Anterior Caudate	brain
14	chr15:78470600-78486600	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr15:78471200-78475800	Strong transcription	Cortex derived primary cultured neurospheres	brain
16	chr15:78472400-78475400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:78473600-78477200	Weak transcription	Spleen	Spleen
18	chr15:78473800-78474800	Weak transcription	Thymus	Thymus
19	chr15:78474200-78474600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
20	chr15:78474200-78474800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:78474400-78474600	Active TSS	HepG2	liver
22	chr15:78474400-78474800	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
23	chr15:78474400-78475000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin

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