Variant report

Variant	rs12148386
Chromosome Location	chr15:77254544-77254545
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	chr15:77240619..77242509-chr15:77252756..77255459,2	MCF-7	breast:
2	chr15:77237875..77240141-chr15:77253920..77256491,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs12438362	0.88[ASN][1000 genomes]
rs12441484	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs12441855	0.83[ASN][1000 genomes]
rs12595586	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs12909665	0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs12912465	0.82[YRI][hapmap]
rs12913810	0.82[ASN][1000 genomes]
rs12916324	0.82[ASN][1000 genomes]
rs17380507	1.00[ASW][hapmap];0.90[CHB][hapmap];0.81[CHD][hapmap];0.83[JPT][hapmap];0.93[LWK][hapmap];0.97[MKK][hapmap];0.82[TSI][hapmap];0.91[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs17464903	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs17465692	0.81[MKK][hapmap]
rs2137307	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs2469204	0.89[CHB][hapmap];0.89[JPT][hapmap];0.85[ASN][1000 genomes]
rs34338978	0.88[ASN][1000 genomes]
rs34748201	0.90[ASN][1000 genomes]
rs35076986	0.85[ASN][1000 genomes]
rs35157989	0.84[ASN][1000 genomes]
rs35999717	0.85[ASN][1000 genomes]
rs3829489	0.90[ASN][1000 genomes]
rs4360890	0.82[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.82[ASN][1000 genomes]
rs4383105	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4886503	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.94[JPT][hapmap];0.81[MKK][hapmap];1.00[YRI][hapmap]
rs4886507	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.94[JPT][hapmap];0.85[LWK][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs4886829	0.82[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs4886839	0.81[ASN][1000 genomes]
rs56234001	0.87[ASN][1000 genomes]
rs58889902	0.82[ASN][1000 genomes]
rs66508953	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs71398948	0.80[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs7166156	0.85[ASN][1000 genomes]
rs7169663	0.85[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.85[ASN][1000 genomes]
rs7174673	1.00[ASW][hapmap];0.82[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.94[JPT][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap]
rs8024737	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8028294	0.82[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap]
rs869884	0.82[TSI][hapmap]
rs9788684	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	esv2758388	chr15:77170550-77373448	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Active TSS 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	18 gene(s)	inside rSNPs	diseases
5	esv2760041	chr15:77170550-77373448	Enhancers Genic enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
6	nsv833058	chr15:77235895-77393640	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv517068	chr15:77254544-77381222	Enhancers Weak transcription Genic enhancers Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12148386	SCAPER	cis	lung	GTEx
rs12148386	PKM2	cis	parietal	SCAN
rs12148386	ULK3	cis	parietal	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
2	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
3	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
4	chr15:77225400-77255400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:77229400-77255000	Weak transcription	Gastric	stomach
6	chr15:77241400-77256000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
7	chr15:77243800-77256000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr15:77243800-77256200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr15:77244000-77256000	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr15:77244000-77256000	Weak transcription	NH-A	brain
11	chr15:77244000-77256800	Weak transcription	Primary T cells from cord blood	blood
12	chr15:77247600-77256200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr15:77252000-77259000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr15:77252000-77259600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:77253000-77255200	Enhancers	Ovary	ovary
16	chr15:77253400-77255000	Enhancers	Skeletal Muscle Male	skeletal muscle
17	chr15:77253400-77256000	Enhancers	Fetal Muscle Leg	muscle
18	chr15:77253600-77256800	Enhancers	Rectal Smooth Muscle	rectum
19	chr15:77253800-77254600	Enhancers	Right Atrium	heart
20	chr15:77253800-77255800	Enhancers	HSMMtube	muscle
21	chr15:77253800-77256000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:77254000-77254600	Enhancers	Stomach Smooth Muscle	stomach
23	chr15:77254200-77254800	Enhancers	Adipose Nuclei	Adipose
24	chr15:77254200-77259600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:77254400-77254600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr15:77254400-77254600	Enhancers	Colon Smooth Muscle	Colon
27	chr15:77254400-77254600	Enhancers	GM12878-XiMat	blood
28	chr15:77254400-77255000	Enhancers	Primary B cells from peripheral blood	blood
29	chr15:77254400-77256000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:77254400-77256200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:77254400-77256200	Enhancers	Left Ventricle	heart
32	chr15:77254400-77256400	Enhancers	Psoas Muscle	Psoas

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