Variant report

Variant	rs7180484
Chromosome Location	chr15:75115416-75115417
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:75115359-75115829	K562	blood:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr15:75113859..75115829-chr15:75135120..75137203,2	MCF-7	breast:
2	chr15:75115096..75116793-chr15:75116936..75121281,3	K562	blood:
3	chr15:75115272..75120114-chr15:75130983..75135707,7	K562	blood:
4	chr15:75113543..75115731-chr15:75122217..75124290,2	K562	blood:
5	chr15:75108017..75109912-chr15:75114230..75116710,2	MCF-7	breast:

No data

Variant related genes	Relation type
CPLX3	TF binding region
LMAN1L	TF binding region
ENSG00000140474	Chromatin interaction
ENSG00000261606	Chromatin interaction
ENSG00000213578	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs11072509	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11634474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12441505	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442901	0.90[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.82[MKK][hapmap];0.86[TSI][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1350193	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1378938	0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1543927	0.91[CEU][hapmap]
rs1869959	0.86[CEU][hapmap]
rs2071501	0.84[CHB][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2168519	0.95[CEU][hapmap];0.90[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301249	0.93[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.98[TSI][hapmap];0.93[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3784790	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3935077	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4886406	0.91[CEU][hapmap]
rs4886615	0.81[ASW][hapmap];0.83[CEU][hapmap];0.95[GIH][hapmap];0.95[LWK][hapmap];0.92[MKK][hapmap];0.82[TSI][hapmap];0.82[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs4886619	0.93[ASW][hapmap];0.91[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.91[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4886629	0.95[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6495126	0.88[GIH][hapmap]
rs6495127	0.88[GIH][hapmap]
rs7085	0.87[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.98[TSI][hapmap];0.89[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7162232	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7176022	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72625792	0.81[ASN][1000 genomes]
rs72730503	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7497201	0.88[GIH][hapmap]
rs8031937	0.88[GIH][hapmap]
rs8033381	0.80[ASW][hapmap];0.95[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.81[MKK][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8042694	0.88[GIH][hapmap]
rs9210	0.81[ASW][hapmap];0.91[CEU][hapmap];0.97[GIH][hapmap];0.95[LWK][hapmap];0.90[MKK][hapmap];0.82[TSI][hapmap]
rs936226	0.95[CEU][hapmap];0.81[CHB][hapmap];0.93[YRI][hapmap];0.85[EUR][1000 genomes]
rs936228	0.82[CEU][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.81[EUR][1000 genomes]
rs936229	0.82[CEU][hapmap];0.95[GIH][hapmap];0.91[LWK][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs936230	0.87[CEU][hapmap];0.88[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv904380	chr15:74869438-75142761	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	69 gene(s)	inside rSNPs	diseases
2	nsv833055	chr15:74988344-75166288	Weak transcription Active TSS Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
3	nsv520527	chr15:75108636-75122856	Enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
4	nsv904381	chr15:75108636-75242155	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	55 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7180484	MPI	cis	lymphoblastoid	seeQTL
rs7180484	MPI	cis	parietal	SCAN
rs7180484	MPI	Cis_1M	lymphoblastoid	RTeQTL
rs7180484	ULK3	cis	multi-tissue	Pritchard
rs7180484	SCAMP2	cis	parietal	SCAN
rs7180484	ULK3	cis	Whole Blood	GTEx
rs7180484	SCAMP5	cis	cerebellum	SCAN
rs7180484	COX5A	Cis_1M	lymphoblastoid	RTeQTL
rs7180484	NEO1	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75109800-75116800	Weak transcription	Brain Anterior Caudate	brain
2	chr15:75111400-75128000	Weak transcription	Gastric	stomach
3	chr15:75113600-75118600	Weak transcription	Right Atrium	heart
4	chr15:75114400-75118200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr15:75115200-75117800	Weak transcription	Spleen	Spleen

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