Variant report

Variant	rs11204712
Chromosome Location	chr1:150690224-150690225
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 21 )
Associated
traits (count: 16 )

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

rs_ID	r²[population]
rs10888388	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11204693	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11204695	0.88[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11204702	0.92[AFR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11204725	0.82[ASN][1000 genomes]
rs1136774	0.82[ASN][1000 genomes]
rs11800059	0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12130363	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12403609	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12568757	0.90[ASN][1000 genomes]
rs34002273	0.81[ASN][1000 genomes]
rs4970924	0.92[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4970926	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6587520	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6694531	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7520022	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7534124	0.80[AFR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv872418	chr1:150683512-150860471	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs11204712	RNU6-1042P	cis	Esophagus Mucosa	GTEx
rs11204712	GOLPH3L	cis	Skin Sun Exposed Lower leg	GTEx
rs11204712	CTSS	cis	Nerve Tibial	GTEx
rs11204712	HORMAD1	cis	Esophagus Mucosa	GTEx
rs11204712	RP11-316M1.12	cis	Esophagus Muscularis	GTEx
rs11204712	ARNT	Cis_1M	lymphoblastoid	RTeQTL
rs11204712	RP11-316M1.12	cis	Adipose Subcutaneous	GTEx
rs11204712	HORMAD1	cis	Adipose Subcutaneous	GTEx
rs11204712	RP11-316M1.12	cis	Nerve Tibial	GTEx
rs11204712	HORMAD1	cis	Skin Sun Exposed Lower leg	GTEx
rs11204712	CTSK	Cis_1M	lymphoblastoid	RTeQTL
rs11204712	CTSS	Cis_1M	lymphoblastoid	RTeQTL
rs11204712	GOLPH3L	cis	Nerve Tibial	GTEx
rs11204712	RP11-316M1.12	cis	Whole Blood	GTEx
rs11204712	RP11-316M1.12	cis	Thyroid	GTEx
rs11204712	HORMAD1	cis	Nerve Tibial	GTEx

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:150670600-150702600	Weak transcription	Hela-S3	cervix
2	chr1:150679200-150698600	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:150681600-150702600	Weak transcription	A549	lung

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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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