Variant report

Variant	rs2959004
Chromosome Location	chr15:74621541-74621542
allele	A/T
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	chr15:74618878..74621837-chr15:74625148..74627418,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11072478	0.94[ASW][hapmap];0.88[CEU][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.94[MKK][hapmap];0.83[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11072479	0.89[EUR][1000 genomes]
rs11634685	0.84[MEX][hapmap]
rs12438594	0.82[YRI][hapmap]
rs12440952	0.81[CEU][hapmap]
rs12913682	0.84[EUR][1000 genomes]
rs12914852	0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12916123	0.96[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs12916765	0.82[ASN][1000 genomes]
rs1484216	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1564782	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]
rs1843090	0.96[CEU][hapmap];0.91[TSI][hapmap];0.90[EUR][1000 genomes]
rs1843091	0.96[CEU][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2277601	1.00[CEU][hapmap];0.90[JPT][hapmap];0.93[EUR][1000 genomes]
rs2277602	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2277605	0.93[EUR][1000 genomes]
rs2277606	0.98[EUR][1000 genomes]
rs2279356	1.00[CEU][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.90[JPT][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes]
rs2279357	0.96[CEU][hapmap];0.91[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2279378	0.80[MEX][hapmap]
rs2415239	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2930291	0.84[MEX][hapmap]
rs2930300	0.88[CEU][hapmap];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2930301	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2930302	0.88[CEU][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2930304	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2930305	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2930306	0.96[CEU][hapmap];0.81[LWK][hapmap];0.93[TSI][hapmap];0.90[EUR][1000 genomes]
rs2959002	0.89[EUR][1000 genomes]
rs2959003	0.81[EUR][1000 genomes]
rs2959005	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2959006	0.88[CEU][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2959007	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2959008	0.88[CEU][hapmap];0.92[MEX][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2959011	0.81[CEU][hapmap]
rs351184	0.84[MEX][hapmap]
rs3825944	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs397074	0.83[ASN][1000 genomes]
rs4077581	0.84[ASW][hapmap];1.00[CEU][hapmap];0.86[CHB][hapmap];0.90[CHD][hapmap];0.88[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077582	1.00[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4077584	0.82[YRI][hapmap]
rs4598865	0.83[ASW][hapmap];0.82[YRI][hapmap]
rs6495096	0.96[CEU][hapmap];0.90[EUR][1000 genomes]
rs68021814	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7173655	0.80[EUR][1000 genomes]
rs7174179	0.96[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs733434	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8031121	0.84[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap]
rs8031424	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs900798	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs900799	0.81[CEU][hapmap]
rs900800	0.80[CEU][hapmap]
rs900802	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]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2959004	SLC2A3	trans	brain	seeQTL
rs2959004	CYP1A2	cis	cerebellum	SCAN
rs2959004	RPLP1	cis	parietal	SCAN
rs2959004	C15orf39	cis	cerebellum	SCAN

Chromatin state (count:10 , 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	chr15:74617000-74622000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr15:74619600-74626400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr15:74620200-74621800	Enhancers	Fetal Thymus	thymus
6	chr15:74620400-74622800	Weak transcription	Placenta	Placenta
7	chr15:74620800-74621800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:74621200-74622200	Weak transcription	Spleen	Spleen
9	chr15:74621400-74622400	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr15:74621400-74623400	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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