Variant report

Variant	rs2638244
Chromosome Location	chr12:40572224-40572225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	12:40570708-40576790..12:40691796-40694737	K562	blood:
2	12:40570708-40576790..12:40703633-40711447	K562	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10878123	0.90[JPT][hapmap]
rs10878208	0.95[CEU][hapmap];0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11175256	0.90[JPT][hapmap]
rs11175332	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11175371	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs11175401	0.90[JPT][hapmap];0.83[ASN][1000 genomes]
rs11175405	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11175422	0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs11175458	0.89[ASN][1000 genomes]
rs11175540	0.86[ASN][1000 genomes]
rs11175558	0.91[CHB][hapmap];0.95[JPT][hapmap]
rs11564115	0.90[JPT][hapmap]
rs12581617	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1472117	0.90[JPT][hapmap]
rs1491922	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1491923	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1491924	0.85[CHD][hapmap];0.90[JPT][hapmap];0.85[ASN][1000 genomes]
rs1491925	0.99[ASN][1000 genomes]
rs1491942	0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs17443199	0.90[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs17461429	0.83[ASN][1000 genomes]
rs2046931	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131088	0.90[JPT][hapmap]
rs2201144	0.90[JPT][hapmap]
rs2253736	0.86[ASN][1000 genomes]
rs2638224	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2638247	0.99[ASN][1000 genomes]
rs2638250	0.94[ASN][1000 genomes]
rs2638268	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2638269	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2638270	0.91[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2638271	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.94[ASN][1000 genomes]
rs2708404	0.83[ASW][hapmap];0.94[LWK][hapmap];0.86[MKK][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes]
rs2708437	0.90[JPT][hapmap]
rs2708438	0.90[JPT][hapmap]
rs2708463	0.94[ASN][1000 genomes]
rs2708465	0.97[ASN][1000 genomes]
rs2708478	0.94[ASN][1000 genomes]
rs2723269	0.90[JPT][hapmap]
rs28365179	0.85[JPT][hapmap]
rs72644819	0.86[ASN][1000 genomes]
rs7310104	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs949640	0.82[CHD][hapmap];0.90[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv899030	chr12:40509341-40580440	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	nsv899031	chr12:40520684-40580440	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1045516	chr12:40543200-40589557	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	n/a
5	esv3398206	chr12:40556364-40581392	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	n/a

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2638244	LRRK2	cis	cerebellum	SCAN
rs2638244	SLC2A13	cis	parietal	SCAN
rs2638244	KIF21A	cis	cerebellum	SCAN
rs2638244	RP11-476D10.1	cis	Whole Blood	GTEx
rs2638244	LRRK2	cis	parietal	SCAN

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

No data

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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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