Variant report

Variant	rs2800485
Chromosome Location	chr10:38542588-38542589
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	chr10:38542504-38542659	Gliobla	brain:	n/a	n/a

Variant related genes	Relation type
ENSG00000234941	TF binding region

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1548255	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs176838	0.96[CEU][hapmap];0.91[CHB][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.85[TSI][hapmap]
rs176879	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs176880	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs176885	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs176886	0.91[CHB][hapmap];0.87[JPT][hapmap]
rs176887	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs176889	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs1892144	0.82[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];0.81[YRI][hapmap]
rs2021650	1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap]
rs2145672	0.90[CHB][hapmap]
rs2472175	0.96[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap]
rs2472177	0.94[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.90[TSI][hapmap];0.96[YRI][hapmap]
rs2474565	0.96[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs2474568	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.88[MEX][hapmap];0.88[TSI][hapmap]
rs2474570	1.00[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap]
rs2474573	0.87[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.91[LWK][hapmap];0.89[YRI][hapmap]
rs2504141	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]
rs2505192	0.86[JPT][hapmap]
rs2505193	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2505194	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.81[CHD][hapmap];0.82[GIH][hapmap];0.87[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap]
rs2505196	0.96[CEU][hapmap];0.91[CHB][hapmap];0.87[JPT][hapmap]
rs2505202	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.88[MEX][hapmap];0.96[YRI][hapmap]
rs2505203	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2754353	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2754360	1.00[CHB][hapmap];0.95[JPT][hapmap];0.92[YRI][hapmap]
rs2754361	0.88[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.87[LWK][hapmap];0.83[MKK][hapmap];0.93[YRI][hapmap]
rs2754495	0.88[ASW][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.81[JPT][hapmap];0.83[LWK][hapmap]
rs2804641	0.85[CEU][hapmap];0.91[CHB][hapmap];0.81[JPT][hapmap]
rs2804649	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs2804675	1.00[CHB][hapmap];0.91[JPT][hapmap];0.93[YRI][hapmap]
rs496627	0.81[CHD][hapmap];0.87[GIH][hapmap]
rs7915062	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];0.88[MEX][hapmap];0.87[MKK][hapmap];0.96[YRI][hapmap]

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	nsv895030	chr10:37715737-38674609	Weak transcription Active TSS Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
2	nsv540566	chr10:38301001-38680127	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv947858	chr10:38516576-38632253	ZNF genes & repeats Active TSS Enhancers	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2800485	HSD17B7P2	cis	parietal	SCAN
rs2800485	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2800485	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2800485	ZNF25	cis	cerebellum	SCAN
rs2800485	NFIL3	trans	lymphoblastoid	seeQTL
rs2800485	HSD17B7P2	cis	Whole Blood	GTEx

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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