Variant report

Variant	rs2841543
Chromosome Location	chr6:13502428-13502429
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:13500313..13502729-chr6:13573324..13575697,3	K562	blood:
2	chr6:13495546..13497355-chr6:13501574..13503680,2	MCF-7	breast:
3	chr6:13485409..13487937-chr6:13501624..13503350,2	K562	blood:

Variant related genes	Relation type
ENSG00000145990	Chromatin interaction
ENSG00000237786	Chromatin interaction
ENSG00000187461	Chromatin interaction
ENSG00000124523	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:69)

rs_ID	r²[population]
rs2081874	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs2115063	0.85[GIH][hapmap]
rs2494775	0.93[CHB][hapmap];0.88[JPT][hapmap];0.88[ASN][1000 genomes]
rs2560767	0.84[ASN][1000 genomes]
rs2560774	0.89[ASN][1000 genomes]
rs2560775	0.83[CEU][hapmap];0.93[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.81[TSI][hapmap];0.89[ASN][1000 genomes]
rs2560776	0.83[CEU][hapmap];0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2560777	0.96[ASN][1000 genomes]
rs2560778	0.96[ASN][1000 genomes]
rs2560780	0.96[ASN][1000 genomes]
rs2560781	0.96[ASN][1000 genomes]
rs2560784	0.97[ASN][1000 genomes]
rs2560786	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2560787	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560789	0.81[CEU][hapmap];0.93[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs2560790	0.88[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.98[ASN][1000 genomes]
rs2560791	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs2560793	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560794	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2560796	0.98[ASN][1000 genomes]
rs2560797	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2560798	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2560799	0.95[ASN][1000 genomes]
rs2560800	0.94[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2560802	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560803	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2560804	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2560806	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841526	0.89[ASN][1000 genomes]
rs2841527	0.89[ASN][1000 genomes]
rs2841528	0.82[CEU][hapmap];0.92[CHB][hapmap];0.89[CHD][hapmap];0.94[JPT][hapmap];0.83[TSI][hapmap];0.89[ASN][1000 genomes]
rs2841530	0.95[ASN][1000 genomes]
rs2841531	0.91[ASN][1000 genomes]
rs2841532	0.97[ASN][1000 genomes]
rs2841533	0.98[ASN][1000 genomes]
rs2841535	0.98[ASN][1000 genomes]
rs2841536	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2841537	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2841539	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2841540	0.98[ASN][1000 genomes]
rs2841542	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841544	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841545	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841569	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4340988	0.96[ASN][1000 genomes]
rs4512205	0.96[ASN][1000 genomes]
rs4715370	0.98[ASN][1000 genomes]
rs4715371	0.98[ASN][1000 genomes]
rs4715372	0.98[ASN][1000 genomes]
rs4715373	0.96[ASN][1000 genomes]
rs4715374	0.96[ASN][1000 genomes]
rs4715376	0.93[ASN][1000 genomes]
rs4715379	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.90[ASN][1000 genomes]
rs4715380	0.90[ASN][1000 genomes]
rs59610068	0.98[ASN][1000 genomes]
rs60499941	0.98[ASN][1000 genomes]
rs6458898	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs6923024	0.86[ASN][1000 genomes]
rs6939496	0.86[ASN][1000 genomes]
rs9370167	0.98[ASN][1000 genomes]
rs9370168	0.98[ASN][1000 genomes]
rs9370171	0.98[ASN][1000 genomes]
rs9370172	0.97[ASN][1000 genomes]
rs9382156	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9382170	0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs9382172	0.98[ASN][1000 genomes]
rs9382174	0.95[ASN][1000 genomes]
rs9382205	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532021	chr6:13232627-13805381	Active TSS Genic enhancers Strong transcription Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	74 gene(s)	inside rSNPs	diseases
2	nsv1033620	chr6:13419730-13571788	Weak transcription Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv462640	chr6:13426539-13519434	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
4	nsv600994	chr6:13426539-13519434	Bivalent/Poised TSS Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv470802	chr6:13441424-13519371	Weak transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2841543	C6orf114	cis	lymphoblastoid	seeQTL

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:13496800-13505400	Weak transcription	Left Ventricle	heart
2	chr6:13499800-13504600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr6:13500200-13512600	Weak transcription	Small Intestine	intestine

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