Variant report

Variant	rs4132535
Chromosome Location	chr15:73357951-73357952
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73355443..73358020-chr15:73360429..73361989,2	MCF-7	breast:
2	chr15:73356525..73360663-chr15:73369090..73372368,3	MCF-7	breast:

Extended variants
information (count: 64 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1023924	0.83[CHD][hapmap]
rs1038137	0.83[JPT][hapmap]
rs10467948	0.83[JPT][hapmap]
rs10467949	0.93[CHB][hapmap];0.97[CHD][hapmap];0.96[GIH][hapmap];0.94[JPT][hapmap];0.94[ASN][1000 genomes]
rs11632639	1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11856922	0.92[CEU][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12050774	0.80[CHD][hapmap]
rs12050848	0.94[CHB][hapmap];0.88[JPT][hapmap]
rs12708506	0.89[CHB][hapmap];0.89[JPT][hapmap]
rs12899246	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12902768	0.83[CHB][hapmap]
rs12907139	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12916928	1.00[ASN][1000 genomes]
rs13379875	0.80[CHD][hapmap]
rs1479337	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs1479340	0.83[CHB][hapmap];0.97[CHD][hapmap]
rs1564345	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs17762600	0.83[CHD][hapmap]
rs17829830	0.83[CHD][hapmap]
rs1871385	0.83[CHB][hapmap];0.83[CHD][hapmap];0.84[GIH][hapmap]
rs2010793	0.94[ASN][1000 genomes]
rs2046017	0.94[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs2127277	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap]
rs2169951	0.83[JPT][hapmap]
rs2251205	0.94[CHB][hapmap];0.97[CHD][hapmap];0.89[JPT][hapmap]
rs2415147	0.83[CHB][hapmap]
rs28481558	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28743094	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28842482	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2899784	0.83[CHB][hapmap]
rs35060813	0.99[ASN][1000 genomes]
rs3736510	0.83[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap]
rs3784793	0.92[CHB][hapmap];0.88[JPT][hapmap]
rs4132536	0.86[CHD][hapmap];0.83[JPT][hapmap]
rs4625692	0.82[LWK][hapmap]
rs4777582	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4777583	0.98[ASN][1000 genomes]
rs4777589	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4777590	0.83[CHD][hapmap];0.83[JPT][hapmap]
rs4777591	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.93[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs58060856	0.81[ASN][1000 genomes]
rs6416501	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6416502	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6495047	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164894	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168555	0.83[CEU][hapmap];0.85[CHB][hapmap]
rs7169083	0.83[CHB][hapmap]
rs7172021	0.83[CHB][hapmap];0.97[CHD][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7172396	0.82[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs7173142	0.98[ASN][1000 genomes]
rs7175329	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs747872	0.83[CHB][hapmap]
rs747873	0.82[CHB][hapmap];0.83[CHD][hapmap];0.80[GIH][hapmap]
rs7495458	0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026121	0.83[JPT][hapmap]
rs8026579	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042700	0.83[CHB][hapmap]
rs922516	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920186	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3352103	chr15:73191535-73454001	Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv482421	chr15:73279141-73426897	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	7 gene(s)	inside rSNPs	diseases
3	nsv904338	chr15:73313691-73483718	Enhancers Active TSS Strong transcription ZNF genes & repeats Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	nsv517966	chr15:73349633-73488753	Enhancers Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv525462	chr15:73349633-73563495	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4132535	THSD4	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73347000-73358800	Weak transcription	HUES64 Cell Line	embryonic stem cell
2	chr15:73349400-73367000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr15:73352000-73365000	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:73353800-73363400	Weak transcription	Aorta	Aorta
5	chr15:73353800-73366000	Weak transcription	Fetal Intestine Large	intestine
6	chr15:73353800-73367400	Weak transcription	Fetal Intestine Small	intestine
7	chr15:73354000-73359000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:73354400-73364800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:73355000-73358000	Enhancers	Brain Cingulate Gyrus	brain
10	chr15:73355200-73365200	Weak transcription	Sigmoid Colon	Sigmoid Colon
11	chr15:73355600-73365800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr15:73356400-73359000	Weak transcription	Brain Angular Gyrus	brain
13	chr15:73356600-73360200	Weak transcription	Brain Anterior Caudate	brain
14	chr15:73356800-73359000	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:73357600-73358000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr15:73357800-73359400	Enhancers	Brain Substantia Nigra	brain

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