Variant report

Variant	rs12572137
Chromosome Location	chr10:50515246-50515247
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10857468	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12252168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12414082	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12416329	0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12571426	0.92[ASN][1000 genomes]
rs12572851	0.90[GIH][hapmap]
rs12573530	0.92[ASN][1000 genomes]
rs17009950	0.81[GIH][hapmap]
rs17176921	0.81[GIH][hapmap]
rs2377942	0.94[ASN][1000 genomes]
rs34752051	0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34838288	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59753859	0.94[ASN][1000 genomes]
rs61848596	0.97[ASN][1000 genomes]
rs6537530	0.90[ASN][1000 genomes]
rs7088781	0.90[GIH][hapmap]
rs7916111	0.80[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];0.94[ASN][1000 genomes]
rs7923735	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv895375	chr10:50306386-51028871	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
2	nsv534410	chr10:50317458-50826916	Weak transcription Bivalent Enhancer Enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv895376	chr10:50480164-50557211	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12572137	CXCR4	trans	cerebellum	SCAN
rs12572137	PPYR1	cis	cerebellum	SCAN

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:50509200-50515400	Enhancers	Right Ventricle	heart
2	chr10:50509200-50517000	Weak transcription	Pancreas	Pancrea
3	chr10:50512000-50515600	Weak transcription	Fetal Muscle Trunk	muscle
4	chr10:50512000-50519200	Weak transcription	Right Atrium	heart
5	chr10:50512400-50517000	Weak transcription	K562	blood
6	chr10:50512600-50515600	Weak transcription	Fetal Muscle Leg	muscle
7	chr10:50513200-50516400	Genic enhancers	Skeletal Muscle Female	skeletal muscle
8	chr10:50513800-50522000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
9	chr10:50514000-50517000	Weak transcription	Fetal Heart	heart
10	chr10:50514400-50519200	Weak transcription	Psoas Muscle	Psoas
11	chr10:50515200-50518400	Weak transcription	Left Ventricle	heart

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Input of quick search could be:

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

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