Variant report

Variant	rs1564782
Chromosome Location	chr15:74622678-74622679
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:74617190..74619532-chr15:74620304..74624205,4	K562	blood:
2	chr15:74622577..74624588-chr15:74627714..74630586,2	MCF-7	breast:

Extended variants
information (count: 48 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs11072478	0.88[CEU][hapmap];0.84[EUR][1000 genomes]
rs11072479	0.83[EUR][1000 genomes]
rs12440952	0.81[CEU][hapmap];0.84[YRI][hapmap];0.84[AFR][1000 genomes]
rs12914852	0.92[EUR][1000 genomes]
rs12916123	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1484216	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs1564783	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs1843090	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs1843091	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2277601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277602	1.00[CEU][hapmap];0.84[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs2277605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2277606	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279356	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2279357	0.96[CEU][hapmap];0.84[TSI][hapmap];0.85[EUR][1000 genomes]
rs2415239	0.84[EUR][1000 genomes]
rs2930300	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs2930301	0.82[EUR][1000 genomes]
rs2930302	0.88[CEU][hapmap];0.83[TSI][hapmap];0.86[EUR][1000 genomes]
rs2930304	1.00[CEU][hapmap];0.81[CHB][hapmap];0.86[JPT][hapmap];0.96[EUR][1000 genomes]
rs2930305	0.91[EUR][1000 genomes]
rs2930306	0.96[CEU][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2959002	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2959003	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2959004	1.00[CEU][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2959005	0.86[EUR][1000 genomes]
rs2959006	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2959007	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2959008	0.88[CEU][hapmap];0.83[TSI][hapmap];0.88[EUR][1000 genomes]
rs2959011	0.81[CEU][hapmap]
rs4077581	1.00[CEU][hapmap];0.82[JPT][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs4077582	1.00[CEU][hapmap];0.82[JPT][hapmap];0.90[EUR][1000 genomes]
rs6495096	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs68021814	0.88[EUR][1000 genomes]
rs7173655	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7174179	0.96[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes]
rs733434	0.88[EUR][1000 genomes]
rs751527	0.87[AFR][1000 genomes]
rs751528	0.82[EUR][1000 genomes]
rs8031121	0.84[CEU][hapmap]
rs8031424	1.00[CEU][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs900798	0.85[EUR][1000 genomes]
rs900799	0.81[CEU][hapmap]
rs900800	0.80[CEU][hapmap]
rs900802	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]

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	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
2	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
3	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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1564782	C15orf39	cis	cerebellum	SCAN
rs1564782	RPLP1	cis	parietal	SCAN
rs1564782	CYP1A2	cis	cerebellum	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:74604800-74623400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
2	chr15:74612000-74657800	Weak transcription	Right Atrium	heart
3	chr15:74619600-74626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr15:74620400-74622800	Weak transcription	Placenta	Placenta
5	chr15:74621400-74623400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:74622400-74623000	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr15:74622400-74623400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr15:74622600-74638600	Weak transcription	Spleen	Spleen

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links