Variant report

Variant	rs12173797
Chromosome Location	chr6:28022723-28022724
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr6:28022273-28022773	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:28022204..28024125-chr6:28233468..28235109,2	MCF-7	breast:
2	chr6:27856950..27859637-chr6:28022500..28024631,2	K562	blood:

Variant related genes	Relation type
OR2B8P	TF binding region
ENSG00000197062	Chromatin interaction
ENSG00000197153	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1150666	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1150678	0.86[EUR][1000 genomes]
rs1225716	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs149897	0.84[EUR][1000 genomes]
rs149941	0.84[EUR][1000 genomes]
rs149942	0.84[EUR][1000 genomes]
rs149944	0.84[EUR][1000 genomes]
rs149945	0.84[EUR][1000 genomes]
rs149955	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs149958	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149959	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149961	0.81[AFR][1000 genomes]
rs149962	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs149964	0.81[AFR][1000 genomes]
rs149965	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs149972	0.84[EUR][1000 genomes]
rs149978	0.84[EUR][1000 genomes]
rs156734	0.83[EUR][1000 genomes]
rs156738	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs156739	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1631552	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1770131	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs183244	0.86[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs188105	0.86[EUR][1000 genomes]
rs202908	0.81[EUR][1000 genomes]
rs203876	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203877	0.86[EUR][1000 genomes]
rs203882	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203883	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203884	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203892	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs203893	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2622319	0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2791332	0.86[EUR][1000 genomes]
rs476167	0.84[EUR][1000 genomes]
rs536704	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9295760	0.86[EUR][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	nsv966688	chr6:28019147-28028399	Bivalent Enhancer	TF binding region Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
5	esv3334902	chr6:28019790-28022864	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	esv3322200	chr6:28022023-28023271	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
7	esv3390093	chr6:28022023-28024221	Inactive region	TF binding region Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs12173797	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs12173797	AL022393.7	cis	Artery Tibial	GTEx
rs12173797	OR1F12	cis	Thyroid	GTEx
rs12173797	AL022393.7	cis	Nerve Tibial	GTEx
rs12173797	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs12173797	ZNF165	Cis_1M	lymphoblastoid	RTeQTL
rs12173797	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs12173797	AL022393.7	cis	Muscle Skeletal	GTEx
rs12173797	OR2B7P	cis	Thyroid	GTEx
rs12173797	RP5-874C20.3	cis	Nerve Tibial	GTEx
rs12173797	OR2B8P	cis	Thyroid	GTEx
rs12173797	AL022393.7	cis	Heart Left Ventricle	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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