Variant report

Variant	rs2014704
Chromosome Location	chr17:38808249-38808250
allele	A/C
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	CEBPB	chr17:38808030-38808387	K562	blood:	n/a	chr17:38808051-38808062
2	RCOR1	chr17:38808246-38808424	K562	blood:	n/a	n/a
3	TAL1	chr17:38808146-38808519	K562	blood:	n/a	n/a
4	SRF	chr17:38808137-38808468	K562	blood:	n/a	n/a
5	EP300	chr17:38808243-38808923	T-47D	breast:	n/a	n/a
6	EP300	chr17:38808226-38808461	K562	blood:	n/a	n/a
7	EP300	chr17:38808248-38808439	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:38804109..38807700-chr17:38808137..38810271,3	MCF-7	breast:

Variant related genes	Relation type
SMARCE1	TF binding region
ENSG00000073584	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1029792	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048572	0.95[CEU][hapmap];0.83[CHB][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.88[LWK][hapmap];0.94[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1048573	0.95[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11658582	0.89[JPT][hapmap]
rs12943859	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2008469	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2109223	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2159430	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2253717	0.81[EUR][1000 genomes]
rs2315020	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2429549	0.95[CEU][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.92[YRI][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462962	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462963	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462964	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2462970	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2469818	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3752026	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.80[LWK][hapmap];0.84[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4890093	0.81[ASW][hapmap];0.95[CEU][hapmap];0.97[GIH][hapmap];0.89[JPT][hapmap];0.89[MEX][hapmap];0.98[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4890117	0.89[JPT][hapmap]
rs4890119	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503547	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6503549	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7209467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7209735	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.88[JPT][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7210983	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7219483	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223332	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7223354	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs726848	0.90[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap]
rs757411	0.90[GIH][hapmap];0.89[JPT][hapmap]
rs758630	0.81[EUR][1000 genomes]
rs8068721	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8076587	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs917593	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs917595	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9303294	0.93[YRI][hapmap]
rs9896791	1.00[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9900324	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9906785	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9915135	0.94[CEU][hapmap];0.82[CHB][hapmap];0.87[JPT][hapmap];0.82[YRI][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]

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
rs2014704	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs2014704	KRT222	cis	Nerve Tibial	GTEx
rs2014704	KRT24	cis	Esophagus Mucosa	GTEx
rs2014704	CCL4	cis	parietal	SCAN
rs2014704	TBCA	trans	cerebellum	SCAN
rs2014704	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs2014704	KRT32	cis	cerebellum	SCAN
rs2014704	TADA2A	cis	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38805200-38815800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr17:38805400-38808800	Weak transcription	NHLF	lung
3	chr17:38805400-38809400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr17:38805400-38812000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:38805400-38816000	Weak transcription	Primary T cells from cord blood	blood
6	chr17:38805400-38821200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr17:38805600-38809200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr17:38805600-38809400	Weak transcription	NHEK	skin
9	chr17:38805600-38815800	Weak transcription	Liver	Liver
10	chr17:38805600-38819400	Weak transcription	Spleen	Spleen
11	chr17:38805600-38820600	Weak transcription	Brain Anterior Caudate	brain
12	chr17:38805600-38821000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr17:38806200-38809200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr17:38806200-38812600	Weak transcription	Fetal Muscle Leg	muscle
15	chr17:38806400-38809200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr17:38807400-38808400	Enhancers	Fetal Intestine Small	intestine
17	chr17:38807400-38808800	Enhancers	K562	blood
18	chr17:38808200-38808400	Enhancers	Placenta Amnion	Placenta Amnion
19	chr17:38808200-38808600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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