Variant report

Variant	rs149964
Chromosome Location	chr6:28018469-28018470
allele	C/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: 119 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs12173797	0.81[AFR][1000 genomes]
rs12174753	0.80[ASN][1000 genomes]
rs1340004	0.80[ASN][1000 genomes]
rs149899	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs149946	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149947	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149948	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149955	0.85[AFR][1000 genomes]
rs149958	0.89[AFR][1000 genomes]
rs149959	0.87[AFR][1000 genomes]
rs149961	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149962	0.88[AFR][1000 genomes]
rs149965	0.80[AFR][1000 genomes]
rs149968	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149969	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs149970	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs156736	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs156738	0.89[AFR][1000 genomes]
rs156739	0.89[AFR][1000 genomes]
rs156744	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16893666	0.80[ASN][1000 genomes]
rs172166	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs175954	0.81[AFR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17711344	0.80[ASN][1000 genomes]
rs17711801	0.80[ASN][1000 genomes]
rs17774663	0.80[ASN][1000 genomes]
rs183244	0.85[AFR][1000 genomes]
rs1853097	0.80[ASN][1000 genomes]
rs1904840	0.80[ASN][1000 genomes]
rs1947862	0.80[ASN][1000 genomes]
rs1947863	0.80[ASN][1000 genomes]
rs203890	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2273564	0.80[ASN][1000 genomes]
rs2295594	0.80[ASN][1000 genomes]
rs34131763	0.80[ASN][1000 genomes]
rs34171748	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs34466819	0.80[ASN][1000 genomes]
rs34716816	0.80[ASN][1000 genomes]
rs35193936	0.80[ASN][1000 genomes]
rs35512245	0.80[ASN][1000 genomes]
rs36078605	0.80[ASN][1000 genomes]
rs3734573	0.80[ASN][1000 genomes]
rs3757187	0.80[ASN][1000 genomes]
rs3823180	0.80[ASN][1000 genomes]
rs464312	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs469227	0.83[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs4711164	0.80[ASN][1000 genomes]
rs4711165	0.80[ASN][1000 genomes]
rs4713135	0.80[ASN][1000 genomes]
rs4713137	0.80[ASN][1000 genomes]
rs4713141	0.80[ASN][1000 genomes]
rs4713142	0.80[ASN][1000 genomes]
rs4713143	0.80[ASN][1000 genomes]
rs4713144	0.80[ASN][1000 genomes]
rs4713145	0.80[ASN][1000 genomes]
rs4713146	0.80[ASN][1000 genomes]
rs4713148	0.80[ASN][1000 genomes]
rs56310871	0.80[ASN][1000 genomes]
rs56364346	0.80[ASN][1000 genomes]
rs61471148	0.92[ASN][1000 genomes]
rs66529373	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6931858	0.80[ASN][1000 genomes]
rs6934769	0.80[ASN][1000 genomes]
rs6941992	0.80[ASN][1000 genomes]
rs7755442	0.80[ASN][1000 genomes]
rs9295758	0.80[ASN][1000 genomes]
rs9295759	0.80[ASN][1000 genomes]
rs9348789	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9348793	0.80[ASN][1000 genomes]
rs9348794	0.80[ASN][1000 genomes]
rs9348796	0.80[ASN][1000 genomes]
rs9357060	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9357061	0.80[ASN][1000 genomes]
rs9357063	0.80[ASN][1000 genomes]
rs9366715	0.80[ASN][1000 genomes]
rs9368549	0.80[ASN][1000 genomes]
rs9368550	0.80[ASN][1000 genomes]
rs9368551	0.80[ASN][1000 genomes]
rs9368552	0.80[ASN][1000 genomes]
rs9368553	0.80[ASN][1000 genomes]
rs9368554	0.80[ASN][1000 genomes]
rs9368555	0.80[ASN][1000 genomes]
rs9380045	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9380047	0.80[ASN][1000 genomes]
rs9380049	0.80[ASN][1000 genomes]
rs9380050	0.80[ASN][1000 genomes]
rs9380052	0.80[ASN][1000 genomes]
rs9380054	0.80[ASN][1000 genomes]
rs9380055	0.80[ASN][1000 genomes]
rs9380056	0.80[ASN][1000 genomes]
rs9380057	0.80[ASN][1000 genomes]
rs9393881	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9393885	0.80[ASN][1000 genomes]
rs9393886	0.80[ASN][1000 genomes]
rs9393888	0.80[ASN][1000 genomes]
rs9393890	0.80[ASN][1000 genomes]
rs9393891	0.80[ASN][1000 genomes]
rs9393892	0.80[ASN][1000 genomes]
rs9393893	0.80[ASN][1000 genomes]
rs9393894	0.80[ASN][1000 genomes]
rs9461433	0.80[ASN][1000 genomes]
rs9468271	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468274	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468275	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9468277	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468278	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9468286	0.80[ASN][1000 genomes]
rs9468290	0.80[ASN][1000 genomes]
rs9468292	0.80[ASN][1000 genomes]
rs9468296	0.80[ASN][1000 genomes]
rs9468297	0.80[ASN][1000 genomes]
rs9468298	0.80[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs149964	AL022393.7	cis	Muscle Skeletal	GTEx
rs149964	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149964	OR2B8P	cis	Skin Sun Exposed Lower leg	GTEx
rs149964	OR2B8P	cis	Thyroid	GTEx
rs149964	RP1-265C24.5	cis	Heart Left Ventricle	GTEx
rs149964	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149964	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149964	OR2B7P	cis	Thyroid	GTEx
rs149964	AL022393.7	cis	Nerve Tibial	GTEx

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

No data

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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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