Variant report

Variant	rs149965
Chromosome Location	chr6:28018689-28018690
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:28017721..28019447-chr6:28188224..28189953,2	K562	blood:
2	chr6:28008817..28010926-chr6:28017296..28019171,2	MCF-7	breast:
3	chr6:28012616..28016428-chr6:28017297..28020846,3	K562	blood:

Variant related genes	Relation type
ENSG00000187763	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1150666	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1150678	0.86[EUR][1000 genomes]
rs12173797	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1225716	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149897	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs149941	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149942	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149944	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149945	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149955	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149958	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149959	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149961	0.80[AFR][1000 genomes]
rs149962	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs149964	0.80[AFR][1000 genomes]
rs149972	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149977	0.81[EUR][1000 genomes]
rs149978	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs156734	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs156738	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs156739	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1631552	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs169431	0.82[EUR][1000 genomes]
rs1770131	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs183244	0.85[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs188105	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs202908	0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs203876	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203877	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs203882	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203883	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203884	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203892	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs203893	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2622319	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2791332	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs476167	0.85[EUR][1000 genomes]
rs536704	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9295760	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	nsv883513	chr6:27982152-28033087	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv981052	chr6:27987196-28024382	Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	12 gene(s)	inside rSNPs	diseases
4	esv3472318	chr6:28018055-28021999	Inactive region	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	esv3472317	chr6:28018092-28021986	Inactive region	TF binding region Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3472316	chr6:28018126-28021927	Inactive region	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	esv3472320	chr6:28018126-28021927	Inactive region	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs149965	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs149965	OR1F12	cis	Thyroid	GTEx
rs149965	ZNF165	Cis_1M	lymphoblastoid	RTeQTL
rs149965	OR2B8P	cis	Thyroid	GTEx
rs149965	AL022393.7	cis	Muscle Skeletal	GTEx
rs149965	OR2B7P	cis	Thyroid	GTEx
rs149965	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149965	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149965	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149965	AL022393.7	cis	Artery Tibial	GTEx
rs149965	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149965	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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