Variant report

Variant	rs531325
Chromosome Location	chr10:89931019-89931020
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs11202678	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12264266	0.89[EUR][1000 genomes]
rs1475606	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs472364	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4933473	0.90[EUR][1000 genomes]
rs533648	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs574006	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs600195	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs644440	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs652517	0.94[EUR][1000 genomes]
rs868872	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831940	chr10:89811247-89989199	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS 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
rs531325	HTR7	cis	parietal	SCAN
rs531325	PAPSS2	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:89918200-89937600	Weak transcription	Aorta	Aorta
2	chr10:89922000-89937600	Weak transcription	Thymus	Thymus
3	chr10:89929200-89932400	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr10:89929400-89933400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
5	chr10:89929600-89931200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr10:89929600-89932600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
7	chr10:89929600-89933400	Enhancers	Dnd41	blood
8	chr10:89929800-89931200	Enhancers	Primary T cells fromperipheralblood	blood
9	chr10:89929800-89932400	Enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr10:89929800-89932800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr10:89930000-89932600	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr10:89930000-89932600	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr10:89930200-89932400	Enhancers	Primary T cells from cord blood	blood
14	chr10:89930400-89932400	Enhancers	Primary T killer memory cells from peripheral blood	blood
15	chr10:89930600-89932400	Enhancers	Primary T helper naive cells fromperipheralblood	blood

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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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