Variant report

Variant	rs12943914
Chromosome Location	chr17:17980671-17980672
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:17980284..17981846-chr17:17994472..17997044,2	K562	blood:
2	chr17:17972218..17973793-chr17:17979715..17981759,2	MCF-7	breast:
3	chr17:17979306..17980957-chr17:17981820..17984346,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11650649	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs11652894	0.87[ASN][1000 genomes]
rs12943202	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12943500	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs12948749	0.84[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs12949525	0.81[AMR][1000 genomes]
rs12952818	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2230316	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955351	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955360	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2955371	0.86[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2955382	0.92[ASW][hapmap];0.95[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.82[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];0.97[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4244602	0.82[JPT][hapmap]
rs4341796	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925123	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925129	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs4925130	0.82[JPT][hapmap];0.80[MEX][hapmap]
rs4925138	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs5002487	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs6502625	0.83[CEU][hapmap];0.82[JPT][hapmap]
rs6502629	0.87[CEU][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap]
rs712265	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7207395	0.82[JPT][hapmap]
rs7222480	0.84[MEX][hapmap]
rs7224815	0.87[CEU][hapmap];0.82[JPT][hapmap]
rs72827413	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8065563	0.82[JPT][hapmap];0.83[MEX][hapmap]
rs8070128	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs8078138	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs8078583	0.82[JPT][hapmap]
rs8079418	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs8080823	0.82[JPT][hapmap];0.84[MEX][hapmap]
rs854762	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854764	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854810	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs854813	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs950966	0.82[JPT][hapmap];0.84[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
2	nsv916653	chr17:17651916-18454952	Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	144 gene(s)	inside rSNPs	diseases
3	nsv533142	chr17:17691726-18236686	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	116 gene(s)	inside rSNPs	diseases
4	nsv482879	chr17:17802463-17989273	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases
5	nsv960429	chr17:17951047-18027679	Strong transcription Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
6	nsv482491	chr17:17959577-18153920	Enhancers Genic enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
7	nsv1061162	chr17:17978838-18259234	Flanking Active TSS Weak transcription Genic enhancers Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
8	nsv492305	chr17:17980441-18424702	Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	68 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12943914	SREBF1	cis	Whole Blood	GTEx
rs12943914	TOM1L2	cis	cerebellum	SCAN
rs12943914	DRG2	cis	Thyroid	GTEx
rs12943914	C17orf39	cis	cerebellum	SCAN
rs12943914	TOM1L2	cis	parietal	SCAN

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17974600-17984400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr17:17974600-17986400	Weak transcription	Placenta	Placenta
3	chr17:17978800-17980800	Enhancers	HepG2	liver
4	chr17:17979000-17982400	Weak transcription	K562	blood
5	chr17:17980600-17981600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood

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