Variant report

Variant	rs2754361
Chromosome Location	chr10:38677789-38677790
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs17595292	0.84[ASN][1000 genomes]
rs17595383	0.82[EUR][1000 genomes]
rs17611390	0.81[EUR][1000 genomes]
rs1892144	0.91[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs2145672	0.96[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2754353	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2754356	0.86[AMR][1000 genomes]
rs2754360	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2754363	0.81[AFR][1000 genomes]
rs2754374	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2754493	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2754495	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.92[MEX][hapmap];0.87[MKK][hapmap];0.98[TSI][hapmap];0.86[YRI][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2800485	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]
rs2800551	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2800552	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804622	0.86[AFR][1000 genomes]
rs2804623	0.88[AFR][1000 genomes]
rs2804624	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2804626	0.84[AMR][1000 genomes]
rs2804632	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2804637	0.82[ASN][1000 genomes]
rs2804638	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2804639	0.81[AMR][1000 genomes]
rs2804641	0.91[CHB][hapmap];0.91[JPT][hapmap];0.86[YRI][hapmap]
rs2804649	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2804675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2804677	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3932487	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6482064	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9299772	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[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	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
2	nsv427860	chr10:38588021-38818835	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv895034	chr10:38632352-38743545	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2764202	chr10:38641508-39076221	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv1048953	chr10:38645824-39074038	Weak transcription ZNF genes & repeats Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
6	nsv428230	chr10:38652001-38818835	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv540568	chr10:38666856-38684802	Weak transcription Strong transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	esv2757379	chr10:38677023-38978680	Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
9	esv2759744	chr10:38677023-39154935	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2754361	ZNF37A	cis	lymphoblastoid	seeQTL
rs2754361	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL
rs2754361	HSD17B7P2	cis	Whole Blood	GTEx
rs2754361	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2754361	ZNF25	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38661000-38683400	Weak transcription	Brain Substantia Nigra	brain
2	chr10:38661200-38680400	Weak transcription	GM12878-XiMat	blood

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