Variant report

Variant	rs2505244
Chromosome Location	chr10:38456047-38456048
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 81 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs1138252	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1329786	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1548255	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs176838	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap]
rs176876	0.94[ASN][1000 genomes]
rs176879	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs176880	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs176882	0.94[ASN][1000 genomes]
rs176885	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.96[ASN][1000 genomes]
rs176886	0.87[CHB][hapmap];0.91[JPT][hapmap]
rs176887	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs176889	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs1998062	0.81[ASN][1000 genomes]
rs2008449	0.99[ASN][1000 genomes]
rs2021650	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2023299	0.94[ASN][1000 genomes]
rs2144859	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2178962	0.94[ASN][1000 genomes]
rs2180412	0.80[ASN][1000 genomes]
rs2263162	0.94[ASN][1000 genomes]
rs2263164	0.94[ASN][1000 genomes]
rs2384731	0.87[ASN][1000 genomes]
rs2472150	0.88[CHD][hapmap]
rs2472175	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2472177	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2472178	0.94[ASN][1000 genomes]
rs2472179	0.82[ASN][1000 genomes]
rs2474554	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474564	0.87[ASN][1000 genomes]
rs2474565	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2474568	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2474570	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.89[ASN][1000 genomes]
rs2474572	0.94[ASN][1000 genomes]
rs2474573	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs2474581	0.92[ASN][1000 genomes]
rs2474591	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474596	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474597	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2474610	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2504120	0.94[ASN][1000 genomes]
rs2504121	0.94[ASN][1000 genomes]
rs2504127	0.94[ASN][1000 genomes]
rs2504139	0.94[ASN][1000 genomes]
rs2504141	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.94[ASN][1000 genomes]
rs2505179	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505185	0.92[ASN][1000 genomes]
rs2505190	0.93[ASN][1000 genomes]
rs2505192	0.89[CEU][hapmap];0.82[JPT][hapmap]
rs2505193	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505194	0.91[CHB][hapmap];0.84[CHD][hapmap];0.91[JPT][hapmap]
rs2505196	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs2505198	0.92[ASN][1000 genomes]
rs2505202	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap]
rs2505203	0.82[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs2505235	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505236	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505248	0.81[ASN][1000 genomes]
rs2505249	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505250	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2505251	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505252	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2505258	0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2505259	0.97[ASN][1000 genomes]
rs2754353	0.91[CHB][hapmap]
rs2754495	0.96[CEU][hapmap];0.91[CHB][hapmap];0.89[TSI][hapmap]
rs2800485	1.00[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap]
rs2804641	0.91[CHB][hapmap]
rs496627	0.86[CHD][hapmap]
rs626519	0.86[CHD][hapmap]
rs645064	0.88[CHD][hapmap]
rs6482060	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71491246	0.80[ASN][1000 genomes]
rs7915062	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[ASN][1000 genomes]
rs932538	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv550419	chr10:38311777-38501654	Enhancers Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv895031	chr10:38402789-38464886	ZNF genes & repeats Enhancers Weak transcription Strong transcription Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv895032	chr10:38427708-38498909	Weak transcription ZNF genes & repeats Enhancers Strong transcription Flanking Active TSS	TF binding region CpG island lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv895033	chr10:38432348-38537070	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv947857	chr10:38453951-38497640	Enhancers ZNF genes & repeats Weak transcription	TF binding region CpG island lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2505244	LOC399744	cis	parietal	SCAN
rs2505244	ZNF37A///ZNF37B	Cis_1M	lymphoblastoid	RTeQTL
rs2505244	ZNF37A	cis	lymphoblastoid	seeQTL
rs2505244	ZNF25	cis	cerebellum	SCAN
rs2505244	HSD17B7P2	cis	Esophagus Mucosa	GTEx
rs2505244	HSD17B7///HSD17B7P2///LOC730412	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:38449400-38456800	Weak transcription	Brain Substantia Nigra	brain

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