Variant report

Variant	rs6535830
Chromosome Location	chr4:152900692-152900693
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	chr4:152892401..152894777-chr4:152900381..152902489,2	K562	blood:
2	chr2:85764217..85766872-chr4:152899544..152902513,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000253077	Chromatin interaction
ENSG00000168906	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10213345	0.81[EUR][1000 genomes]
rs10517559	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11099836	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11099838	0.86[ASN][1000 genomes]
rs12503702	0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12645594	0.94[MEX][hapmap]
rs13105209	0.96[ASN][1000 genomes]
rs1385782	0.97[ASN][1000 genomes]
rs1531917	0.94[ASW][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs17028306	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs1813118	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs1872314	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs2406809	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs34493397	0.86[ASN][1000 genomes]
rs35771940	0.82[ASN][1000 genomes]
rs4696120	0.94[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs4696309	0.86[ASN][1000 genomes]
rs7668707	0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs9307889	0.85[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs975820	0.94[ASW][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv432644	chr4:152635395-153023402	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	nsv880341	chr4:152861685-153110256	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv931416	chr4:152877808-153440553	Genic enhancers Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv3466417	chr4:152898480-152901092	ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3466420	chr4:152898521-152901075	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv3466418	chr4:152898548-152901035	Weak transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	esv3466421	chr4:152898625-152900986	ZNF genes & repeats Weak transcription	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6535830	GUCY1A3	cis	cerebellum	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:152899400-152910600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr4:152899600-152904200	Weak transcription	Fetal Brain Male	brain

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