Variant report

Variant	rs2118961
Chromosome Location	chr15:40614200-40614201
allele	C/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:16)
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	CTCF	chr15:40614060-40614210	AG09319	gingival:	n/a	n/a

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40612389..40614304-chr15:40626844..40628895,2	K562	blood:
2	chr15:40573745..40575892-chr15:40613923..40616158,2	K562	blood:
3	chr15:40607352..40610567-chr15:40611377..40615529,4	MCF-7	breast:
4	chr15:40606578..40610704-chr15:40612489..40616999,9	K562	blood:
5	chr15:40596957..40600729-chr15:40613519..40617071,4	K562	blood:
6	chr15:40613571..40616194-chr15:40676591..40679577,2	K562	blood:
7	chr15:40611920..40613859-chr15:40613927..40615590,2	K562	blood:
8	chr15:40573791..40575924-chr15:40613554..40617283,3	MCF-7	breast:
9	chr15:40608873..40611853-chr15:40613878..40616202,2	MCF-7	breast:
10	chr15:40510541..40512947-chr15:40613762..40616049,2	K562	blood:
11	chr15:40606578..40609257-chr15:40612890..40617072,4	K562	blood:
12	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
13	chr15:40599147..40601689-chr15:40614013..40619011,4	K562	blood:
14	chr15:40613324..40616013-chr15:40714259..40715828,2	K562	blood:
15	chr15:40613352..40615012-chr15:40615826..40618374,2	MCF-7	breast:
16	chr15:40613668..40617143-chr15:40761466..40764045,3	K562	blood:

No data

Variant related genes	Relation type
LINC00984	TF binding region
ENSG00000137841	Chromatin interaction
ENSG00000259330	Chromatin interaction
ENSG00000259288	Chromatin interaction
ENSG00000188549	Chromatin interaction
ENSG00000230778	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1077476	0.81[CHB][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.88[AMR][1000 genomes]
rs11070264	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12081	0.95[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes]
rs2289333	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.94[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2289334	0.92[AMR][1000 genomes]
rs4277318	0.94[ASN][1000 genomes]
rs4334271	0.86[JPT][hapmap]
rs4923863	0.89[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs4923864	1.00[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs4924455	0.81[CHB][hapmap];0.90[JPT][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs7164564	0.88[AMR][1000 genomes]
rs7164747	0.94[AMR][1000 genomes]
rs7173747	0.95[CHB][hapmap];0.81[CHD][hapmap];0.90[JPT][hapmap];0.90[MEX][hapmap]
rs748245	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs882829	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs934937	0.86[CHB][hapmap];0.81[JPT][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	esv34145	chr15:40549617-40889824	Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv510660	chr15:40552906-40721883	Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
3	esv1850798	chr15:40560607-40622191	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
4	nsv827305	chr15:40596162-40625922	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2118961	PENK	trans	brain	seeQTL

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40584200-40614800	Weak transcription	Gastric	stomach
2	chr15:40600000-40614600	Weak transcription	Brain Substantia Nigra	brain
3	chr15:40602000-40614600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr15:40602600-40614600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:40606000-40615200	Weak transcription	Psoas Muscle	Psoas
6	chr15:40606600-40615000	Weak transcription	Colonic Mucosa	Colon
7	chr15:40607400-40614600	Weak transcription	Hela-S3	cervix
8	chr15:40607600-40614600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:40607800-40614200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr15:40607800-40614200	Weak transcription	HMEC	breast
11	chr15:40608000-40614600	Weak transcription	HSMM	muscle
12	chr15:40608000-40615000	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:40609400-40614400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:40610600-40614800	Weak transcription	GM12878-XiMat	blood
15	chr15:40610800-40614200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:40612400-40614600	Enhancers	HepG2	liver
17	chr15:40612400-40615600	Enhancers	Fetal Heart	heart
18	chr15:40612600-40614400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:40612600-40615000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr15:40612800-40614200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr15:40613000-40614600	Enhancers	Stomach Smooth Muscle	stomach
22	chr15:40613000-40614800	Enhancers	Colon Smooth Muscle	Colon
23	chr15:40613000-40615000	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr15:40613000-40615200	Enhancers	Primary T killer memory cells from peripheral blood	blood
25	chr15:40613000-40615200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:40613200-40614200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
27	chr15:40613200-40614200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr15:40613200-40614200	Weak transcription	Pancreas	Pancrea
29	chr15:40613200-40614400	Weak transcription	Rectal Smooth Muscle	rectum
30	chr15:40613200-40614400	Weak transcription	Right Ventricle	heart
31	chr15:40613200-40614600	Weak transcription	Primary B cells from peripheral blood	blood
32	chr15:40613200-40614600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr15:40613200-40614600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:40613200-40614800	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr15:40613200-40615200	Weak transcription	Left Ventricle	heart
36	chr15:40613400-40614200	Weak transcription	Fetal Stomach	stomach
37	chr15:40613400-40614400	Weak transcription	Placenta	Placenta
38	chr15:40613400-40614400	Weak transcription	Spleen	Spleen
39	chr15:40613400-40614600	Weak transcription	Fetal Lung	lung
40	chr15:40613400-40615000	Weak transcription	Primary monocytes fromperipheralblood	blood
41	chr15:40613400-40615200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
42	chr15:40613400-40615200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr15:40613400-40615200	Enhancers	K562	blood
44	chr15:40613400-40617000	Enhancers	Fetal Brain Male	brain
45	chr15:40613600-40614200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
46	chr15:40613600-40614200	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:40613600-40614200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
48	chr15:40613600-40614600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:40613600-40614600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr15:40613600-40614600	Weak transcription	Primary T helper naive cells from peripheral blood	blood

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