Variant report

Variant	rs12148488
Chromosome Location	chr15:75382542-75382543
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:75380896..75383442-chr15:75385564..75387083,2	MCF-7	breast:
2	chr15:75382030..75383992-chr15:75492942..75495683,2	K562	blood:

Variant related genes	Relation type
ENSG00000167173	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs11854975	0.86[EUR][1000 genomes]
rs12101482	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899062	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12904227	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12917120	0.82[YRI][hapmap]
rs13056	0.85[YRI][hapmap]
rs1867148	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1867149	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2083730	0.82[LWK][hapmap]
rs2120019	0.82[YRI][hapmap]
rs2304899	0.92[CHB][hapmap];0.84[LWK][hapmap];0.90[YRI][hapmap]
rs2304902	0.80[EUR][1000 genomes]
rs28730367	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34582157	0.87[ASN][1000 genomes]
rs35078352	0.86[EUR][1000 genomes]
rs3812944	0.84[CHB][hapmap];0.82[LWK][hapmap];0.90[YRI][hapmap]
rs3812945	0.88[TSI][hapmap]
rs4886417	0.85[TSI][hapmap]
rs4886648	0.85[TSI][hapmap]
rs4886651	0.82[LWK][hapmap]
rs4886655	0.87[EUR][1000 genomes]
rs6495144	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6495150	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6495151	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs67168917	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163362	0.83[EUR][1000 genomes]
rs7163636	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];0.91[LWK][hapmap];0.88[MEX][hapmap];0.85[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7167261	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7181261	0.81[EUR][1000 genomes]
rs8028632	0.82[YRI][hapmap]
rs8030089	0.81[YRI][hapmap]
rs8039755	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.89[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

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	nsv569993	chr15:75242155-75483752	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	72 gene(s)	inside rSNPs	diseases
2	nsv457205	chr15:75336729-75447773	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
3	nsv569994	chr15:75336729-75447773	Genic enhancers Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv904383	chr15:75382542-75520378	Weak transcription Genic enhancers Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Caffeine consumption	21490707	GWAS catalog

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12148488	SCAMP5	cis	Artery Tibial	GTEx
rs12148488	SCAMP2	cis	parietal	SCAN
rs12148488	POMZP3	trans	lymphoblastoid	seeQTL
rs12148488	ULK3	cis	parietal	SCAN
rs12148488	TLE3	cis	cerebellum	SCAN
rs12148488	CYP11A1	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:75381800-75382600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:75381800-75382800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr15:75381800-75382800	Enhancers	Placenta	Placenta
4	chr15:75381800-75383000	Enhancers	HUVEC	blood vessel
5	chr15:75382000-75382600	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr15:75382200-75382600	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr15:75382200-75382600	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:75382200-75382600	Enhancers	Skeletal Muscle Male	skeletal muscle
9	chr15:75382200-75382800	Enhancers	Brain Anterior Caudate	brain
10	chr15:75382200-75382800	Enhancers	Fetal Muscle Leg	muscle
11	chr15:75382200-75382800	Enhancers	Spleen	Spleen
12	chr15:75382200-75383000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr15:75382200-75383000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr15:75382200-75383000	Enhancers	Primary hematopoietic stem cells	blood
15	chr15:75382200-75383000	Enhancers	K562	blood
16	chr15:75382200-75383200	Enhancers	Adipose Nuclei	Adipose
17	chr15:75382400-75382800	Enhancers	Right Atrium	heart
18	chr15:75382400-75382800	Enhancers	Osteobl	bone
19	chr15:75382400-75383000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
20	chr15:75382400-75383000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr15:75382400-75383000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood

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