Variant report

Variant	rs149898
Chromosome Location	chr6:27958072-27958073
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	chr6:27777496..27780622-chr6:27956410..27960052,3	K562	blood:

Variant related genes	Relation type
ENSG00000203813	Chromatin interaction

Extended variants
information (count: 56 )
Associated
traits (count: 13 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1150676	0.80[YRI][hapmap]
rs1150682	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1150683	0.85[YRI][hapmap]
rs1225593	0.92[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1480646	0.80[YRI][hapmap]
rs149854	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs149879	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs149957	0.85[YRI][hapmap]
rs156741	0.85[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs156742	0.85[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1619221	0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs169263	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs169433	0.85[YRI][hapmap]
rs172164	0.85[YRI][hapmap]
rs175953	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs175955	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1770132	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs183926	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1871695	0.85[YRI][hapmap]
rs200959	0.85[YRI][hapmap]
rs200962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs200970	0.92[YRI][hapmap];1.00[EUR][1000 genomes]
rs203865	0.80[YRI][hapmap]
rs203867	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203870	0.80[YRI][hapmap]
rs203874	0.80[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs203885	0.85[YRI][hapmap]
rs203894	0.80[YRI][hapmap]
rs2200870	1.00[EUR][1000 genomes]
rs2622318	0.92[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2622321	0.80[YRI][hapmap]
rs276364	0.85[YRI][hapmap]
rs276366	0.85[YRI][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276367	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276368	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs276372	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2791334	0.80[YRI][hapmap]
rs366113	0.83[AMR][1000 genomes]
rs425159	1.00[YRI][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs427348	0.85[YRI][hapmap]
rs539474	0.85[YRI][hapmap]
rs56262840	1.00[EUR][1000 genomes]
rs56366090	1.00[EUR][1000 genomes]
rs58700542	1.00[EUR][1000 genomes]
rs60554811	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73740585	1.00[EUR][1000 genomes]
rs73740805	1.00[EUR][1000 genomes]
rs73740842	1.00[EUR][1000 genomes]
rs839777	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9348795	0.85[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 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	nsv1022173	chr6:27734824-27959408	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
3	nsv883512	chr6:27748631-27969004	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	379 gene(s)	inside rSNPs	diseases
4	nsv601208	chr6:27810626-27969004	Active TSS Bivalent/Poised TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	237 gene(s)	inside rSNPs	diseases
5	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
6	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:13)

SNP	Gene	Cis/trans	Tissue	Source
rs149898	TTR	trans	brain	seeQTL
rs149898	CRX	trans	brain	seeQTL
rs149898	GSG1	trans	brain	seeQTL
rs149898	SLC5A7	trans	brain	seeQTL
rs149898	OTX2	trans	brain	seeQTL
rs149898	SH2D2A	trans	brain	seeQTL
rs149898	EMP1	trans	brain	seeQTL
rs149898	PDE6H	trans	brain	seeQTL
rs149898	ASMT	trans	brain	seeQTL
rs149898	LRTM1	trans	brain	seeQTL
rs149898	DDC	trans	brain	seeQTL
rs149898	GUCA1C	trans	brain	seeQTL
rs149898	Hs.158943	cis	multi-tissue	Pritchard

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
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