Variant report

Variant	rs4533765
Chromosome Location	chr4:85915570-85915571
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10029496	0.86[EUR][1000 genomes]
rs10856851	0.88[EUR][1000 genomes]
rs10856852	0.94[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11097026	0.86[EUR][1000 genomes]
rs11097030	0.90[ASN][1000 genomes]
rs11730981	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11732309	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11732347	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12498637	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12498787	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12503215	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12503330	0.80[EUR][1000 genomes]
rs12506456	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12510410	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12640378	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12640811	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12648852	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13109918	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13114115	0.87[EUR][1000 genomes]
rs13118671	0.86[TSI][hapmap]
rs13124246	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13141322	0.88[EUR][1000 genomes]
rs13148035	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1508670	0.85[JPT][hapmap]
rs17009317	0.84[TSI][hapmap]
rs17009341	0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2046404	0.95[JPT][hapmap];0.86[EUR][1000 genomes]
rs2869216	0.86[GIH][hapmap];0.81[JPT][hapmap];0.96[MEX][hapmap]
rs28754901	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34239067	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34314581	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35892581	0.82[EUR][1000 genomes]
rs4131745	0.87[EUR][1000 genomes]
rs4287999	0.91[ASN][1000 genomes]
rs4376130	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4383611	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4464556	0.82[EUR][1000 genomes]
rs4470615	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4590017	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs4624645	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4626191	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4634212	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56094216	0.80[EUR][1000 genomes]
rs56194765	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531777	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6531782	1.00[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6531783	0.84[CHD][hapmap];0.82[JPT][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs6833661	0.88[EUR][1000 genomes]
rs6847067	0.80[JPT][hapmap]
rs6847811	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6858666	0.81[JPT][hapmap];0.96[MEX][hapmap]
rs72664952	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7654035	0.95[JPT][hapmap];0.91[EUR][1000 genomes]
rs7661609	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7663580	0.87[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7675324	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7682896	0.84[EUR][1000 genomes]
rs7690054	0.83[EUR][1000 genomes]
rs7692223	0.82[JPT][hapmap];0.83[EUR][1000 genomes]
rs7694949	0.88[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7699226	0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9684737	0.91[EUR][1000 genomes]
rs9790649	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1829655	chr4:85577491-86292692	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv519588	chr4:85762385-86591202	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
3	esv3367963	chr4:85911017-86246036	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4533765	HERC5	cis	cerebellum	SCAN
rs4533765	NCRNA00247	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:85906800-85927200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:85913400-85926800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
3	chr4:85915000-85915800	Enhancers	Cortex derived primary cultured neurospheres	brain
4	chr4:85915400-85915600	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr4:85915400-85915600	Active TSS	Rectal Smooth Muscle	rectum
6	chr4:85915400-85915600	Active TSS	Right Atrium	heart
7	chr4:85915400-85915800	Active TSS	H1 Cell Line	embryonic stem cell
8	chr4:85915400-85915800	Active TSS	Adipose Nuclei	Adipose
9	chr4:85915400-85915800	Active TSS	Aorta	Aorta
10	chr4:85915400-85915800	Active TSS	Brain Anterior Caudate	brain
11	chr4:85915400-85915800	Active TSS	Duodenum Smooth Muscle	Duodenum
12	chr4:85915400-85915800	Active TSS	Fetal Muscle Trunk	muscle
13	chr4:85915400-85915800	Active TSS	Fetal Muscle Leg	muscle
14	chr4:85915400-85915800	Enhancers	Right Ventricle	heart
15	chr4:85915400-85915800	Active TSS	Stomach Smooth Muscle	stomach

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