Variant report

Variant	rs900802
Chromosome Location	chr15:74628242-74628243
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:74625942..74628669-chr15:74642107..74644237,2	MCF-7	breast:
2	chr15:74625426..74628688-chr15:74630642..74633848,4	MCF-7	breast:
3	chr15:74622577..74624588-chr15:74627714..74630586,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140459	Chromatin interaction
ENSG00000260266	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs11072478	0.89[ASW][hapmap];0.84[CEU][hapmap];0.85[LWK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11072479	0.84[EUR][1000 genomes]
rs12438594	0.82[YRI][hapmap]
rs12913682	0.80[EUR][1000 genomes]
rs12914852	0.87[EUR][1000 genomes]
rs12916123	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1484216	0.83[CEU][hapmap]
rs1564782	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1843090	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs1843091	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2277601	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277602	0.96[CEU][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs2277605	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2277606	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279356	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2279357	0.92[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs2415239	0.88[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs2930300	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2930301	0.89[AFR][1000 genomes];0.83[EUR][1000 genomes]
rs2930302	0.84[CEU][hapmap]
rs2930304	0.96[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.94[EUR][1000 genomes]
rs2930305	0.84[EUR][1000 genomes]
rs2930306	0.92[CEU][hapmap];0.93[TSI][hapmap];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2959002	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2959003	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs2959004	0.94[ASW][hapmap];0.96[CEU][hapmap];0.82[CHD][hapmap];0.89[GIH][hapmap];0.90[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2959006	0.84[CEU][hapmap]
rs2959007	0.84[CEU][hapmap]
rs2959008	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs2959011	0.81[CEU][hapmap]
rs3825944	0.82[YRI][hapmap]
rs4077581	0.96[CEU][hapmap];0.91[GIH][hapmap];0.82[JPT][hapmap];0.98[TSI][hapmap];0.90[EUR][1000 genomes]
rs4077582	0.96[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs4077584	0.82[YRI][hapmap]
rs4598865	0.82[YRI][hapmap]
rs6495096	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs68021814	0.81[EUR][1000 genomes]
rs7173655	0.82[ASN][1000 genomes]
rs7174179	0.92[CEU][hapmap];0.91[TSI][hapmap];0.83[EUR][1000 genomes]
rs733434	0.81[EUR][1000 genomes]
rs8031121	0.80[CEU][hapmap]
rs8031424	0.95[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428641	chr15:74555113-74724630	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	34 gene(s)	inside rSNPs	diseases
2	nsv482615	chr15:74593625-74757962	Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs900802	C15orf39	cis	cerebellum	SCAN
rs900802	CYP1A2	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74612000-74657800	Weak transcription	Right Atrium	heart
2	chr15:74622600-74638600	Weak transcription	Spleen	Spleen
3	chr15:74627400-74631800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:74628000-74628400	Enhancers	Placenta	Placenta
5	chr15:74628000-74642200	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr15:74628200-74629800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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