Variant report

Variant	rs6504872
Chromosome Location	chr17:45438952-45438953
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 57 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs11079774	0.85[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs11079775	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11655943	0.94[ASW][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.81[ASN][1000 genomes]
rs12452315	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12452796	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.83[LWK][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs12453233	0.95[ASN][1000 genomes]
rs12603582	1.00[CHB][hapmap];0.85[CHD][hapmap]
rs1912482	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1912483	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1912487	0.85[CEU][hapmap];0.90[ASN][1000 genomes]
rs2085755	0.86[AFR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2136751	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2175290	0.84[ASW][hapmap];0.82[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.81[TSI][hapmap];0.94[ASN][1000 genomes]
rs2317631	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34537623	0.85[ASN][1000 genomes]
rs35016056	0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3809863	0.94[ASW][hapmap];0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.89[YRI][hapmap];0.81[ASN][1000 genomes]
rs3883319	0.85[ASN][1000 genomes]
rs4338849	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4794058	0.92[CEU][hapmap];0.87[TSI][hapmap]
rs4968317	0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4968319	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.85[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4968320	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56952963	0.94[ASN][1000 genomes]
rs58512566	0.88[ASN][1000 genomes]
rs62076461	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67688344	0.83[ASN][1000 genomes]
rs7206971	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7214410	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.85[TSI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7214468	0.83[YRI][hapmap]
rs9303533	0.81[ASN][1000 genomes]
rs9674670	0.81[ASN][1000 genomes]
rs9889709	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9890782	0.89[ASN][1000 genomes]
rs9892686	0.85[ASN][1000 genomes]
rs9893901	0.84[ASW][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.86[MEX][hapmap];0.92[ASN][1000 genomes]
rs9894905	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9895274	0.86[AFR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9895746	0.94[ASN][1000 genomes]
rs9897492	0.91[ASN][1000 genomes]
rs9900360	0.94[ASN][1000 genomes]
rs9900366	0.90[ASN][1000 genomes]
rs9905581	0.82[CEU][hapmap]
rs9908393	0.83[ASN][1000 genomes]
rs9911944	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9912311	0.85[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs9914653	0.85[ASN][1000 genomes]
rs9915919	0.84[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.81[LWK][hapmap];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1062983	chr17:45030095-45789543	Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
2	nsv1062096	chr17:45416538-45518683	Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv470590	chr17:45419138-45547077	Weak transcription ZNF genes & repeats Bivalent/Poised TSS Strong transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	esv1818362	chr17:45419139-45499396	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv457821	chr17:45419139-45547078	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv575462	chr17:45419139-45547078	Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv516872	chr17:45419139-45702280	Strong transcription Genic enhancers Enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
8	nsv908564	chr17:45422628-45522311	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	esv1801088	chr17:45435575-45522311	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs6504872	C17orf57	cis	cerebellum	SCAN
rs6504872	VPS25	cis	cerebellum	SCAN
rs6504872	DBF4B	cis	cerebellum	SCAN
rs6504872	VPS25	cis	parietal	SCAN
rs6504872	TBKBP1	cis	Artery Tibial	GTEx
rs6504872	RAB5C	cis	parietal	SCAN
rs6504872	C17orf57	cis	parietal	SCAN
rs6504872	TBKBP1	cis	Nerve Tibial	GTEx
rs6504872	TBKBP1	cis	lymphoblastoid	seeQTL
rs6504872	NPEPPS	cis	parietal	SCAN
rs6504872	HOXB2	cis	cerebellum	SCAN
rs6504872	MRPL45P2	cis	lymphoblastoid	seeQTL
rs6504872	NBR2	cis	cerebellum	SCAN
rs6504872	MRPL45P2	cis	Skin Sun Exposed Lower leg	GTEx
rs6504872	KPNB1	Cis_1M	lymphoblastoid	RTeQTL
rs6504872	CDK5RAP3	cis	cerebellum	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45402000-45442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr17:45402200-45446400	Weak transcription	Colon Smooth Muscle	Colon
3	chr17:45402200-45500800	Weak transcription	Aorta	Aorta
4	chr17:45402800-45440800	Weak transcription	Primary T cells from cord blood	blood
5	chr17:45411600-45468200	Weak transcription	Left Ventricle	heart
6	chr17:45412400-45463400	Weak transcription	Gastric	stomach
7	chr17:45413400-45463800	Weak transcription	Ovary	ovary
8	chr17:45421800-45449800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr17:45423000-45450000	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr17:45423000-45465400	Weak transcription	Adipose Nuclei	Adipose
11	chr17:45423200-45450000	Weak transcription	Primary B cells from cord blood	blood
12	chr17:45432600-45439600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr17:45433200-45439800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr17:45434600-45439400	Weak transcription	Fetal Intestine Small	intestine
15	chr17:45435000-45463200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr17:45435200-45447600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr17:45435400-45449600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr17:45438600-45439400	Strong transcription	Primary B cells from peripheral blood	blood

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