Variant report

Variant	rs3906371
Chromosome Location	chr5:112842992-112842993
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:112842312..112845098-chr5:112847464..112851049,4	K562	blood:
2	chr5:112842488..112845098-chr5:112846749..112850121,5	K562	blood:

Variant related genes	Relation type
ENSG00000047188	Chromatin interaction

Extended variants
information (count: 72 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10036300	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs10039853	0.83[JPT][hapmap]
rs10040203	0.84[JPT][hapmap]
rs10045444	0.80[EUR][1000 genomes]
rs10046057	0.84[JPT][hapmap]
rs10079895	0.82[JPT][hapmap]
rs10079973	0.84[JPT][hapmap]
rs10080096	0.84[JPT][hapmap]
rs1017209	0.84[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes]
rs1035408	0.82[AMR][1000 genomes]
rs10477497	0.84[JPT][hapmap]
rs10478127	0.84[JPT][hapmap]
rs10478132	0.84[JPT][hapmap]
rs1052896	0.81[JPT][hapmap]
rs1132528	0.87[CHD][hapmap];0.96[MEX][hapmap];0.83[TSI][hapmap]
rs11956399	0.84[JPT][hapmap]
rs12186798	0.84[JPT][hapmap]
rs12660001	0.81[JPT][hapmap]
rs1593953	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs171181	0.83[AMR][1000 genomes]
rs182987	0.84[AMR][1000 genomes]
rs1833681	0.84[JPT][hapmap]
rs2288449	0.84[JPT][hapmap]
rs2416282	0.88[MEX][hapmap]
rs2431548	0.84[AMR][1000 genomes]
rs2434664	0.83[AMR][1000 genomes]
rs2434665	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs255856	0.88[MEX][hapmap]
rs27566	0.88[MEX][hapmap]
rs2910018	0.80[CHB][hapmap]
rs34075952	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs348933	0.84[AMR][1000 genomes]
rs348949	0.83[AMR][1000 genomes]
rs348950	0.83[AMR][1000 genomes]
rs348953	0.83[AMR][1000 genomes]
rs3857435	0.88[MEX][hapmap]
rs3857437	1.00[CEU][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3909887	0.86[AFR][1000 genomes]
rs423089	0.83[AMR][1000 genomes]
rs4324667	0.83[EUR][1000 genomes]
rs4398627	0.83[GIH][hapmap];0.81[TSI][hapmap]
rs459428	0.81[AMR][1000 genomes]
rs4639215	0.87[CHD][hapmap];0.96[MEX][hapmap]
rs465898	0.81[AMR][1000 genomes]
rs4705557	0.84[JPT][hapmap]
rs4705825	0.84[JPT][hapmap]
rs4705827	0.84[JPT][hapmap]
rs4705828	0.82[JPT][hapmap]
rs6594721	0.84[JPT][hapmap]
rs6594732	0.84[JPT][hapmap]
rs6594734	0.84[JPT][hapmap]
rs675353	0.96[MEX][hapmap];0.83[AMR][1000 genomes]
rs6886628	0.84[JPT][hapmap]
rs6887816	0.84[JPT][hapmap]
rs6889574	0.84[JPT][hapmap]
rs7349799	0.81[JPT][hapmap]
rs7705562	0.84[JPT][hapmap]
rs7706958	0.84[JPT][hapmap]
rs7709110	0.84[JPT][hapmap]
rs7711078	0.82[JPT][hapmap]
rs7711367	0.84[JPT][hapmap]
rs7713038	0.84[JPT][hapmap]
rs7713348	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7727449	0.83[GIH][hapmap];0.86[JPT][hapmap];0.81[TSI][hapmap]
rs7729306	0.84[JPT][hapmap]
rs7730802	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7737023	0.84[JPT][hapmap]
rs929774	0.84[JPT][hapmap]
rs9326895	0.87[CHD][hapmap];0.96[MEX][hapmap]
rs9552	0.87[CHD][hapmap];0.91[MEX][hapmap]
rs9654519	0.82[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv599396	chr5:112408944-112853189	Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs3906371	YTHDC2	cis	cerebellum	SCAN
rs3906371	YTHDC2	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112841400-112847800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:112841400-112848000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr5:112841600-112844200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112841600-112847000	Weak transcription	NHEK	skin
5	chr5:112842200-112844200	Weak transcription	HMEC	breast
6	chr5:112842800-112843600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood

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