Variant report

Variant	rs17602500
Chromosome Location	chr3:143666017-143666018
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	chr3:143665083..143667441-chr3:143670165..143673071,2	K562	blood:
2	chr3:143665779..143667511-chr3:143689617..143691914,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000181744	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1025984	0.80[CHD][hapmap];0.88[MEX][hapmap]
rs10513234	0.94[CHB][hapmap];0.90[JPT][hapmap];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10513235	0.94[CHB][hapmap];0.90[CHD][hapmap];0.90[JPT][hapmap]
rs1125704	0.81[CEU][hapmap]
rs13064130	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs13078840	0.94[CHB][hapmap];0.90[CHD][hapmap];0.86[JPT][hapmap]
rs13081286	0.84[CEU][hapmap]
rs1466941	0.81[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17667256	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs1979910	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap]
rs1992093	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.87[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2279856	1.00[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2885197	0.85[ASN][1000 genomes]
rs34038325	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34071449	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34402874	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35072578	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35211123	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35362423	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs35692092	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35716467	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4315684	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4446205	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4535221	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4563409	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59287916	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60505453	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62267390	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6440210	0.94[CHB][hapmap];1.00[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs6767811	0.81[CEU][hapmap]
rs6768153	0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs721572	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.91[MKK][hapmap];0.93[TSI][hapmap]
rs723491	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7610378	0.94[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.88[MEX][hapmap]
rs7634145	0.84[CEU][hapmap]
rs9683376	0.81[CEU][hapmap]

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	nsv877568	chr3:143621140-143992630	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	esv3365190	chr3:143642195-143925886	Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
3	nsv591922	chr3:143645242-143825439	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs17602500	TM4SF18	cis	cerebellum	SCAN
rs17602500	HPS3	cis	cerebellum	SCAN
rs17602500	C3orf58	cis	cerebellum	SCAN
rs17602500	CHST2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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