Variant report

Variant	rs4705821
Chromosome Location	chr5:112773784-112773785
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	chr5:112773432..112776218-chr5:112822998..112825663,2	MCF-7	breast:
2	chr5:112767090..112769759-chr5:112772592..112775569,2	K562	blood:

Variant related genes	Relation type
ENSG00000171444	Chromatin interaction
ENSG00000232633	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:95)

rs_ID	r²[population]
rs10036300	0.91[JPT][hapmap]
rs10039853	0.90[JPT][hapmap]
rs10040203	0.91[JPT][hapmap]
rs10046057	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs10061552	0.83[JPT][hapmap]
rs10063334	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10071816	0.82[MEX][hapmap]
rs10074538	0.93[EUR][1000 genomes]
rs10079603	0.83[JPT][hapmap]
rs10079895	0.90[JPT][hapmap]
rs10079973	0.91[JPT][hapmap]
rs10080096	0.91[JPT][hapmap]
rs1017209	0.81[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs10477497	0.91[JPT][hapmap]
rs10477499	1.00[JPT][hapmap]
rs10477500	1.00[JPT][hapmap]
rs10478127	0.91[JPT][hapmap]
rs10478129	1.00[JPT][hapmap]
rs10478132	0.91[JPT][hapmap]
rs1052896	0.81[JPT][hapmap]
rs11241214	0.83[JPT][hapmap];0.86[MEX][hapmap]
rs11241215	1.00[JPT][hapmap]
rs11738075	0.80[CEU][hapmap]
rs11749931	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs11750488	0.87[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs11956399	0.91[JPT][hapmap]
rs12186798	0.91[JPT][hapmap]
rs12660001	0.89[JPT][hapmap]
rs13362066	1.00[JPT][hapmap]
rs1833681	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs2248930	1.00[YRI][hapmap]
rs2288449	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs26991	0.82[CHB][hapmap];0.89[YRI][hapmap]
rs348928	1.00[YRI][hapmap]
rs348929	0.96[YRI][hapmap]
rs348931	0.88[YRI][hapmap]
rs348932	1.00[YRI][hapmap]
rs348938	1.00[YRI][hapmap]
rs348947	1.00[YRI][hapmap]
rs348956	1.00[YRI][hapmap]
rs348961	1.00[YRI][hapmap]
rs348962	1.00[YRI][hapmap]
rs348963	1.00[YRI][hapmap]
rs367943	1.00[YRI][hapmap]
rs3763138	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs3763140	1.00[JPT][hapmap]
rs3815911	0.81[JPT][hapmap]
rs3842917	0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs3936061	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs4334877	1.00[JPT][hapmap]
rs444322	1.00[YRI][hapmap]
rs455435	1.00[YRI][hapmap]
rs463167	1.00[YRI][hapmap]
rs463249	1.00[YRI][hapmap]
rs4705557	0.91[JPT][hapmap]
rs4705820	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4705823	1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4705825	0.81[GIH][hapmap];0.91[JPT][hapmap];0.83[MEX][hapmap]
rs4705827	0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs4705828	1.00[JPT][hapmap]
rs57530930	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60810500	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs644154	1.00[YRI][hapmap]
rs6594718	0.88[CHB][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs6594719	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6594720	0.83[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6594721	0.83[ASW][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.91[MEX][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap]
rs6594732	0.91[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs6594733	0.81[JPT][hapmap];0.91[MEX][hapmap];0.82[YRI][hapmap]
rs6594734	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs6864278	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6865809	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs6877432	0.91[JPT][hapmap]
rs6883383	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs6886628	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs6887816	0.91[JPT][hapmap];1.00[YRI][hapmap]
rs6889574	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs6898425	0.83[JPT][hapmap]
rs7349799	0.89[JPT][hapmap]
rs7705562	0.91[JPT][hapmap]
rs7706796	0.87[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7706958	0.91[JPT][hapmap]
rs7709110	1.00[ASW][hapmap];1.00[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7711078	0.90[JPT][hapmap]
rs7711211	0.83[JPT][hapmap];0.86[MEX][hapmap]
rs7711367	0.91[JPT][hapmap];0.86[MEX][hapmap]
rs7713038	0.91[JPT][hapmap]
rs7713451	1.00[JPT][hapmap];0.91[MEX][hapmap]
rs7729306	0.91[JPT][hapmap];0.91[MEX][hapmap]
rs7730801	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7730949	1.00[JPT][hapmap];0.82[MEX][hapmap]
rs7737023	0.91[JPT][hapmap]
rs919304	1.00[JPT][hapmap];0.86[MEX][hapmap]
rs929774	0.91[JPT][hapmap];0.81[YRI][hapmap]
rs9326893	1.00[JPT][hapmap]

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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs4705821	KCNN2	cis	cerebellum	SCAN
rs4705821	YTHDC2	cis	cerebellum	SCAN
rs4705821	YTHDC2	cis	parietal	SCAN
rs4705821	CDO1	cis	cerebellum	SCAN
rs4705821	YTHDC2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:112762000-112786000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr5:112764400-112779200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr5:112764600-112786400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr5:112764800-112786800	Weak transcription	NHEK	skin
5	chr5:112770200-112773800	Enhancers	Fetal Stomach	stomach
6	chr5:112770400-112783400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr5:112770600-112786800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr5:112772000-112775200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
9	chr5:112773600-112773800	Enhancers	Fetal Brain Male	brain
10	chr5:112773600-112774800	Weak transcription	Fetal Heart	heart

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