Variant report

Variant	rs10519952
Chromosome Location	chr4:149201414-149201415
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs11099686	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs11099687	0.90[CEU][hapmap];1.00[CHB][hapmap]
rs12498662	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17024541	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17484245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17581605	0.81[CHB][hapmap]
rs3752701	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.95[ASN][1000 genomes]
rs3846322	0.82[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.83[MKK][hapmap];0.95[ASN][1000 genomes]
rs3846329	0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[TSI][hapmap]
rs3910047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.80[JPT][hapmap]
rs3925570	0.94[CEU][hapmap];1.00[CHB][hapmap]
rs4835133	0.91[ASW][hapmap];0.88[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.83[MEX][hapmap];0.92[MKK][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs59896839	0.87[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61349394	0.95[ASN][1000 genomes]
rs6535599	0.93[CEU][hapmap];1.00[CHB][hapmap]
rs6855341	0.83[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.83[LWK][hapmap];0.89[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72491781	0.91[AFR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1027263	chr4:149127120-149320135	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv537296	chr4:149127120-149320135	Flanking Active TSS Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1031815	chr4:149172485-149282928	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv527076	chr4:149196991-149201619	Weak transcription Enhancers	n/a	n/a	inside rSNPs	diseases
5	nsv1028105	chr4:149199913-149284620	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv537297	chr4:149199913-149284620	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10519952	OTUD4	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:149192400-149209400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr4:149194400-149216400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr4:149195000-149204200	Weak transcription	Brain Cingulate Gyrus	brain
4	chr4:149195200-149203600	Weak transcription	Duodenum Smooth Muscle	Duodenum
5	chr4:149195200-149207600	Weak transcription	Brain Angular Gyrus	brain
6	chr4:149195600-149203200	Weak transcription	Right Ventricle	heart
7	chr4:149195600-149203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr4:149195600-149204000	Weak transcription	Brain Anterior Caudate	brain
9	chr4:149195800-149203600	Weak transcription	Liver	Liver
10	chr4:149195800-149205000	Weak transcription	Gastric	stomach
11	chr4:149196200-149203800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr4:149196800-149202800	Weak transcription	Fetal Heart	heart
13	chr4:149196800-149209600	Weak transcription	Pancreas	Pancrea
14	chr4:149197400-149203800	Weak transcription	Stomach Mucosa	stomach
15	chr4:149198000-149203200	Weak transcription	Fetal Intestine Large	intestine
16	chr4:149199200-149203200	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr4:149199600-149209600	Weak transcription	Left Ventricle	heart
18	chr4:149199800-149203600	Weak transcription	Psoas Muscle	Psoas

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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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