Variant report

Variant	rs12438362
Chromosome Location	chr15:77243990-77243991
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77237726..77240574-chr15:77240909..77244202,4	K562	blood:
2	chr15:77237726..77241253-chr15:77241760..77244409,3	K562	blood:
3	chr15:77224050..77226260-chr15:77243934..77246089,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000117906	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12148386	0.88[ASN][1000 genomes]
rs12441855	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595586	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909665	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913810	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916324	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17380507	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17464903	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs34338978	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34748201	0.95[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35076986	0.94[ASN][1000 genomes]
rs35157989	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999717	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3829489	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4360890	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886507	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886839	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56234001	0.95[ASN][1000 genomes]
rs58889902	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66508953	0.90[ASN][1000 genomes]
rs71398948	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166156	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7169663	0.82[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8024737	0.90[ASN][1000 genomes]
rs9788684	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs12438362	SCAPER	cis	Thyroid	GTEx
rs12438362	SCAPER	cis	Nerve Tibial	GTEx
rs12438362	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs12438362	SCAPER	cis	lung	GTEx
rs12438362	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
2	chr15:77225000-77245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:77225000-77245200	Weak transcription	Esophagus	oesophagus
4	chr15:77225000-77247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
6	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
7	chr15:77225200-77245200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:77225200-77246400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:77225400-77255400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:77225800-77244600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr15:77225800-77245000	Weak transcription	Fetal Heart	heart
12	chr15:77226200-77247200	Weak transcription	Fetal Brain Male	brain
13	chr15:77228200-77245600	Weak transcription	HMEC	breast
14	chr15:77229200-77245200	Weak transcription	Small Intestine	intestine
15	chr15:77229200-77251600	Weak transcription	NHLF	lung
16	chr15:77229400-77249000	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr15:77229400-77254400	Weak transcription	Psoas Muscle	Psoas
18	chr15:77229400-77255000	Weak transcription	Gastric	stomach
19	chr15:77230200-77245400	Weak transcription	K562	blood
20	chr15:77231400-77246400	Weak transcription	GM12878-XiMat	blood
21	chr15:77231400-77251800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:77231600-77247200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr15:77233800-77253400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
24	chr15:77234600-77244200	Strong transcription	HUES64 Cell Line	embryonic stem cell
25	chr15:77234800-77246600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr15:77235200-77244000	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:77235600-77244000	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr15:77235800-77244000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr15:77237200-77253000	Weak transcription	Ovary	ovary
30	chr15:77238200-77247000	Weak transcription	Fetal Kidney	kidney
31	chr15:77238600-77246800	Weak transcription	Rectal Smooth Muscle	rectum
32	chr15:77238800-77246600	Weak transcription	Colon Smooth Muscle	Colon
33	chr15:77239800-77244000	Strong transcription	NH-A	brain
34	chr15:77240000-77244000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
35	chr15:77240000-77246800	Weak transcription	Primary hematopoietic stem cells	blood
36	chr15:77240600-77244200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr15:77241400-77256000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:77241600-77245400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
39	chr15:77241600-77253800	Weak transcription	HSMMtube	muscle
40	chr15:77241800-77244800	Weak transcription	HepG2	liver
41	chr15:77241800-77246000	Weak transcription	NHDF-Ad	bronchial
42	chr15:77242000-77245200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr15:77242000-77247600	Weak transcription	NHEK	skin
44	chr15:77242000-77250800	Weak transcription	Skeletal Muscle Female	skeletal muscle
45	chr15:77242200-77246800	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr15:77242600-77244600	Weak transcription	HUVEC	blood vessel
47	chr15:77242600-77245800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:77242800-77245600	Weak transcription	Hela-S3	cervix
49	chr15:77242800-77251800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
50	chr15:77243000-77244000	Genic enhancers	Ganglion Eminence derived primary cultured neurospheres	brain

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