Variant report

Variant	rs34338978
Chromosome Location	chr15:77226805-77226806
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:77222885..77225072-chr15:77226205..77228462,2	K562	blood:
2	chr15:77224127..77226874-chr15:77232246..77234714,2	K562	blood:
3	chr15:77226311..77228173-chr15:77229637..77231808,2	K562	blood:

Variant related genes	Relation type
ENSG00000117906	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs12148386	0.88[ASN][1000 genomes]
rs12438362	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12441855	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12595586	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12909665	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12913810	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916324	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17380507	0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17464903	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34748201	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35076986	0.93[ASN][1000 genomes]
rs35157989	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35999717	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3829489	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4360890	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4886507	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4886839	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56234001	0.95[ASN][1000 genomes]
rs58889902	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66508953	0.90[ASN][1000 genomes]
rs71398948	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7166156	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7169663	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8024737	0.90[ASN][1000 genomes]
rs9788684	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[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	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

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs34338978	SCAPER	Cis_1M	lymphoblastoid	RTeQTL
rs34338978	SCAPER	cis	lung	GTEx
rs34338978	SCAPER	cis	Thyroid	GTEx
rs34338978	SCAPER	cis	Nerve Tibial	GTEx
rs34338978	SCAPER	cis	Artery Tibial	GTEx

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77224800-77227800	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:77224800-77228800	Weak transcription	Gastric	stomach
3	chr15:77224800-77231000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:77224800-77243000	Weak transcription	Lung	lung
5	chr15:77224800-77256000	Weak transcription	Pancreas	Pancrea
6	chr15:77225000-77227200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr15:77225000-77227800	Weak transcription	Ovary	ovary
8	chr15:77225000-77227800	Weak transcription	Psoas Muscle	Psoas
9	chr15:77225000-77227800	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:77225000-77227800	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr15:77225000-77227800	Weak transcription	Stomach Smooth Muscle	stomach
12	chr15:77225000-77228000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr15:77225000-77228000	Weak transcription	Left Ventricle	heart
14	chr15:77225000-77228400	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr15:77225000-77228800	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr15:77225000-77240400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:77225000-77240400	Weak transcription	Spleen	Spleen
18	chr15:77225000-77241000	Weak transcription	Colonic Mucosa	Colon
19	chr15:77225000-77242800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr15:77225000-77243000	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:77225000-77245200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr15:77225000-77245200	Weak transcription	Esophagus	oesophagus
23	chr15:77225000-77247000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
24	chr15:77225000-77254600	Weak transcription	Aorta	Aorta
25	chr15:77225000-77260200	Weak transcription	Right Ventricle	heart
26	chr15:77225200-77227600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:77225200-77227600	Weak transcription	Fetal Kidney	kidney
28	chr15:77225200-77227600	Weak transcription	HSMMtube	muscle
29	chr15:77225200-77227800	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr15:77225200-77245200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr15:77225200-77246400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
32	chr15:77225400-77227000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:77225400-77227200	Weak transcription	GM12878-XiMat	blood
34	chr15:77225400-77227600	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr15:77225400-77227600	Weak transcription	Rectal Smooth Muscle	rectum
36	chr15:77225400-77227600	Weak transcription	K562	blood
37	chr15:77225400-77227600	Weak transcription	NHEK	skin
38	chr15:77225400-77227800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
39	chr15:77225400-77227800	Weak transcription	NHLF	lung
40	chr15:77225400-77228000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr15:77225400-77228000	Weak transcription	HMEC	breast
42	chr15:77225400-77231400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr15:77225400-77232400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:77225400-77238000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:77225400-77238800	Weak transcription	Stomach Mucosa	stomach
46	chr15:77225400-77255400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr15:77225600-77227600	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:77225600-77227600	Weak transcription	Brain Angular Gyrus	brain
49	chr15:77225600-77227800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:77225600-77227800	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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