Variant report

Variant	rs6875999
Chromosome Location	chr5:95470989-95470990
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 23 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10073752	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs10073810	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10515232	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs17085333	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3777165	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3777166	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3777171	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3777173	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs3777175	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs4330486	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4365863	0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4538631	0.82[CEU][hapmap];0.91[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap]
rs58666663	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66853776	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6865400	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6881872	0.82[CHB][hapmap];0.94[JPT][hapmap]
rs72656691	0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72656692	0.98[EUR][1000 genomes];0.97[ASN][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	esv2758003	chr5:95231706-95540433	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
2	esv2759355	chr5:95231706-95540433	Weak transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	20 gene(s)	inside rSNPs	diseases
3	esv2757121	chr5:95304236-95539536	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
4	nsv1030444	chr5:95353620-95995619	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases
5	nsv537810	chr5:95353620-95995619	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6875999	RIOK2	cis	cerebellum	SCAN
rs6875999	TTC37	cis	cerebellum	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:95461600-95482000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr5:95465800-95477600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:95470400-95475800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr5:95470400-95482000	Weak transcription	HSMM	muscle
5	chr5:95470400-95485800	Weak transcription	HSMMtube	muscle
6	chr5:95470600-95471600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr5:95470800-95477400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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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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