Variant report

Variant	rs12403609
Chromosome Location	chr1:150676485-150676486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 18 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10888388	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204693	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11204695	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11204702	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204712	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11204725	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs1136774	0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs11800059	0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12130363	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12568757	0.88[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs34593358	0.85[AFR][1000 genomes]
rs4970924	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4970926	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6587520	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6694531	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66958685	0.85[AFR][1000 genomes]
rs7520022	1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7534124	0.80[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs9733	0.87[AFR][1000 genomes]

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	nsv1006838	chr1:150440214-150722783	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	175 gene(s)	inside rSNPs	diseases
2	esv2829859	chr1:150608894-150937329	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
3	nsv872417	chr1:150618632-150759979	Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv1014638	chr1:150647987-150679033	Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv437158	chr1:150652202-150683512	Enhancers Flanking Active TSS Active TSS Strong transcription Genic enhancers Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:18)

SNP	Gene	Cis/trans	Tissue	Source
rs12403609	ARNT	cis	Thyroid	GTEx
rs12403609	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs12403609	RP11-316M1.12	cis	Thyroid	GTEx
rs12403609	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs12403609	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs12403609	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs12403609	RP11-316M1.12	cis	Whole Blood	GTEx
rs12403609	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs12403609	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs12403609	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs12403609	CTSS	cis	multi-tissue	Pritchard
rs12403609	GOLPH3L	cis	Nerve Tibial	GTEx
rs12403609	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs12403609	CTSS	cis	Nerve Tibial	GTEx
rs12403609	HORMAD1	cis	Nerve Tibial	GTEx
rs12403609	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs12403609	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs12403609	HORMAD1	cis	Esophagus Mucosa	GTEx

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150670600-150677400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:150670600-150681200	Weak transcription	A549	lung
3	chr1:150670600-150681400	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr1:150670600-150702600	Weak transcription	Hela-S3	cervix
5	chr1:150675400-150676600	Enhancers	GM12878-XiMat	blood
6	chr1:150675400-150677400	Strong transcription	Monocytes-CD14+_RO01746	blood
7	chr1:150675800-150676600	Weak transcription	Pancreatic Islets	Pancreatic Islet

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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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