Variant report

Variant	rs8074758
Chromosome Location	chr17:38820241-38820242
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	POLR2A	chr17:38820161-38820380	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38813785..38815529-chr17:38818795..38820329,2	K562	blood:

Variant related genes	Relation type
ENSG00000271876	TF binding region

Extended variants
information (count: 46 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11078950	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11650910	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11654834	0.94[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.81[LWK][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11659024	0.81[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.92[YRI][hapmap]
rs11869540	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1474454	1.00[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.86[LWK][hapmap];0.95[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1526601	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16966093	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1961204	0.84[EUR][1000 genomes]
rs2011870	0.91[EUR][1000 genomes]
rs2272288	0.82[EUR][1000 genomes]
rs2429547	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2429548	0.88[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2429550	0.84[EUR][1000 genomes]
rs2429551	0.95[CEU][hapmap];0.83[JPT][hapmap];0.84[EUR][1000 genomes]
rs2429552	0.92[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap]
rs2462957	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462960	0.83[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462961	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2462965	0.83[EUR][1000 genomes]
rs2462966	0.96[CEU][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2462967	0.82[EUR][1000 genomes]
rs2462969	0.92[CEU][hapmap];0.86[JPT][hapmap];0.80[EUR][1000 genomes]
rs2469817	0.96[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];0.95[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2469819	0.80[EUR][1000 genomes]
rs2469820	0.96[CEU][hapmap];0.95[CHD][hapmap];0.87[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.84[EUR][1000 genomes]
rs2469825	1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs55664118	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6503545	0.96[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6503546	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs67138687	0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs723728	0.92[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.82[TSI][hapmap];0.82[EUR][1000 genomes]
rs723729	0.92[CEU][hapmap];0.90[CHD][hapmap];0.82[GIH][hapmap];0.86[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap]
rs726849	0.92[CEU][hapmap];0.86[JPT][hapmap]
rs8065040	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs874889	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs887376	0.96[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9303294	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9630729	0.80[AFR][1000 genomes];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9675112	0.89[CEU][hapmap];0.86[JPT][hapmap]
rs9894823	0.86[CHB][hapmap];0.91[JPT][hapmap];0.92[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv431626	chr17:38770965-38999722	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
5	nsv908225	chr17:38776406-38868480	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs8074758	SPRY2	trans	lymphoblastoid	seeQTL
rs8074758	KRT24	cis	Esophagus Mucosa	GTEx
rs8074758	TADA2A	cis	cerebellum	SCAN
rs8074758	CCL4	cis	parietal	SCAN
rs8074758	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs8074758	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs8074758	SMARCE1	cis	multi-tissue	Pritchard
rs8074758	SLFN11	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38805400-38821200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:38805600-38820600	Weak transcription	Brain Anterior Caudate	brain
3	chr17:38805600-38821000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr17:38808400-38821000	Weak transcription	Fetal Intestine Small	intestine
5	chr17:38810000-38820800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr17:38816800-38821200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr17:38819600-38821000	Weak transcription	HUES6 Cell Line	embryonic stem cell
8	chr17:38819600-38821600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr17:38819800-38820600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr17:38819800-38820600	Enhancers	Pancreatic Islets	Pancreatic Islet
11	chr17:38819800-38821000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr17:38819800-38821000	Weak transcription	Brain Angular Gyrus	brain
13	chr17:38819800-38821200	Weak transcription	Spleen	Spleen
14	chr17:38820000-38821000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr17:38820000-38821000	Enhancers	Liver	Liver

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