Variant report

Variant	rs149962
Chromosome Location	chr6:28015918-28015919
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:27859381..27860988-chr6:28015377..28018182,2	K562	blood:
2	chr6:28015384..28017168-chr6:28019091..28020593,2	K562	blood:

Variant related genes	Relation type
ENSG00000233224	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1150666	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1150678	0.86[EUR][1000 genomes]
rs12173797	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1225716	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149897	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149899	0.87[AFR][1000 genomes]
rs149941	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149942	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149944	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149945	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149955	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149958	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149959	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149961	0.88[AFR][1000 genomes]
rs149964	0.88[AFR][1000 genomes]
rs149965	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149972	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs149977	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs149978	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs156734	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs156738	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs156739	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1631552	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs169431	0.83[EUR][1000 genomes]
rs172166	0.86[AFR][1000 genomes]
rs1770131	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs183244	0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs188105	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs202908	0.85[AFR][1000 genomes];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs203876	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203877	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203882	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203883	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203884	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203890	0.87[AFR][1000 genomes]
rs203892	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs203893	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2622319	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2791332	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs476167	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs536704	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9295760	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9348789	0.84[AFR][1000 genomes]
rs9357060	0.85[AFR][1000 genomes]
rs9380045	0.82[AFR][1000 genomes]
rs9393881	0.85[AFR][1000 genomes]
rs9468271	0.85[AFR][1000 genomes]
rs9468274	0.83[AFR][1000 genomes]
rs9468275	0.85[AFR][1000 genomes]
rs9468277	0.85[AFR][1000 genomes]
rs9468278	0.85[AFR][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	nsv1022651	chr6:27864217-28017997	Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
2	nsv830619	chr6:27872302-28062544	Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs149962	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs149962	ZNF165	Cis_1M	lymphoblastoid	RTeQTL
rs149962	OR1F12	cis	Thyroid	GTEx
rs149962	OR2B7P	cis	Thyroid	GTEx
rs149962	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149962	OR2B8P	cis	Thyroid	GTEx
rs149962	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149962	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149962	AL022393.7	cis	Muscle Skeletal	GTEx
rs149962	AL022393.7	cis	Artery Tibial	GTEx
rs149962	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149962	AL022393.7	cis	Nerve Tibial	GTEx

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

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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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