Variant report

Variant	rs149948
Chromosome Location	chr6:27974817-27974818
allele	C/G
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	chr6:27970175-27975350	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:27972416..27975036-chr6:27975260..27977885,2	MCF-7	breast:
2	chr6:27969309..27971948-chr6:27974273..27976504,2	K562	blood:
3	chr6:27933640..27936048-chr6:27973424..27976149,2	K562	blood:

Variant related genes	Relation type
IQCB2P	TF binding region

Extended variants
information (count: 29 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs149855	0.83[EUR][1000 genomes]
rs149897	0.83[AFR][1000 genomes]
rs149899	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs149941	0.87[AFR][1000 genomes]
rs149942	0.87[AFR][1000 genomes]
rs149944	0.87[AFR][1000 genomes]
rs149945	0.87[AFR][1000 genomes]
rs149946	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149947	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149961	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149964	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs149968	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs149969	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs149970	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs149972	0.93[AFR][1000 genomes]
rs156734	0.85[AFR][1000 genomes]
rs156736	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs156744	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs172166	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs200969	0.84[EUR][1000 genomes]
rs200978	0.84[EUR][1000 genomes]
rs203890	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34171748	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs464312	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469227	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs573179	0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432858	chr6:27719375-28011652	Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	387 gene(s)	inside rSNPs	diseases
2	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
3	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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs149948	AL022393.7	cis	Nerve Tibial	GTEx
rs149948	RP1-265C24.5	cis	Heart Left Ventricle	GTEx
rs149948	BTN3A2///BTN3A3	Cis_chr	lymphoblastoid	RTeQTL
rs149948	OR2B8P	cis	Thyroid	GTEx
rs149948	BTN3A2	Cis_chr	lymphoblastoid	RTeQTL
rs149948	RP1-265C24.5	cis	Muscle Skeletal	GTEx
rs149948	AL022393.7	cis	Muscle Skeletal	GTEx
rs149948	AL022393.7	cis	Heart Left Ventricle	GTEx
rs149948	AL022393.7	cis	Artery Aorta	GTEx
rs149948	OR2B7P	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:27974800-27975000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links