Variant report

Variant	rs11540714
Chromosome Location	chr15:40617124-40617125
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:4)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:4 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAZ	chr15:40614373-40617806	IMR90	lung:	n/a	chr15:40614503-40614513 chr15:40617461-40617470
2	MXI1	chr15:40615137-40617187	SK-N-SH	brain:	n/a	n/a
3	SIN3A	chr15:40614717-40617191	H1-hESC	embryonic stem cell:	n/a	chr15:40615806-40615817 chr15:40615521-40615532
4	STAT3	chr15:40617062-40617220	MCF10A-Er-Src	breast:	n/a	n/a

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40615499..40617257-chr15:40732436..40735160,2	K562	blood:
2	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
3	chr15:40616209..40618065-chr15:40641977..40644316,2	MCF-7	breast:
4	chr15:40616336..40620318-chr15:40620739..40624439,7	MCF-7	breast:
5	chr15:40573791..40575924-chr15:40613554..40617283,3	MCF-7	breast:
6	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
7	chr15:40599147..40601689-chr15:40614013..40619011,4	K562	blood:
8	chr15:40613668..40617143-chr15:40761466..40764045,3	K562	blood:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PHGR1-1	chr15:40616681-40618914	NONHSAT041825
2	lnc-PHGR1-1	chr15:40616696-40617689	NONHSAT041826

No data

Variant related genes	Relation type
LINC00984	TF binding region
ENSG00000252714	Chromatin interaction
ENSG00000140320	Chromatin interaction
ENSG00000233041	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000230778	Chromatin interaction
ENSG00000188549	Chromatin interaction
ENSG00000169105	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs2008462	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945670	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044352	1.00[ASN][1000 genomes]
rs56232597	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56289107	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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	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
5	esv3378883	chr15:40614885-40617433	Active TSS Bivalent Enhancer Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	esv3428901	chr15:40615210-40617508	Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Weak transcription	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
7	esv3438791	chr15:40615285-40617833	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11540714	KNSTRN	cis	Artery Aorta	GTEx
rs11540714	KNSTRN	cis	Esophagus Muscularis	GTEx
rs11540714	KNSTRN	cis	Whole Blood	GTEx
rs11540714	KNSTRN	cis	Artery Tibial	GTEx
rs11540714	KNSTRN	cis	Heart Left Ventricle	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40614800-40617200	Active TSS	Gastric	stomach
2	chr15:40614800-40618200	Active TSS	Colon Smooth Muscle	Colon
3	chr15:40614800-40618400	Active TSS	Aorta	Aorta
4	chr15:40615000-40617200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:40615200-40617200	Active TSS	H9 Cell Line	embryonic stem cell
6	chr15:40615200-40617200	Active TSS	Pancreatic Islets	Pancreatic Islet
7	chr15:40615200-40617800	Active TSS	Right Atrium	heart
8	chr15:40615400-40617200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr15:40615400-40617200	Active TSS	Primary mononuclear cells fromperipheralblood	Blood
10	chr15:40615400-40617200	Active TSS	Esophagus	oesophagus
11	chr15:40615400-40617200	Active TSS	Sigmoid Colon	Sigmoid Colon
12	chr15:40615400-40617600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:40615400-40617600	Active TSS	Left Ventricle	heart
14	chr15:40615400-40618000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
15	chr15:40615400-40618400	Active TSS	Right Ventricle	heart
16	chr15:40615600-40617200	Active TSS	Liver	Liver
17	chr15:40615600-40617200	Active TSS	Lung	lung
18	chr15:40615600-40617200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr15:40615600-40617200	Active TSS	HSMM	muscle
20	chr15:40615600-40617200	Active TSS	HSMMtube	muscle
21	chr15:40615600-40617200	Active TSS	Osteobl	bone
22	chr15:40615600-40617400	Active TSS	Pancreas	Pancrea
23	chr15:40615600-40617800	Active TSS	Ovary	ovary
24	chr15:40615800-40617200	Active TSS	HMEC	breast
25	chr15:40615800-40618000	Flanking Active TSS	Primary hematopoietic stem cells	blood
26	chr15:40616200-40617200	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
27	chr15:40616200-40617200	Flanking Active TSS	Dnd41	blood
28	chr15:40616200-40617400	Active TSS	GM12878-XiMat	blood
29	chr15:40616400-40617200	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr15:40616400-40617200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
31	chr15:40616400-40617400	Flanking Active TSS	Primary B cells from cord blood	blood
32	chr15:40616400-40618200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:40616400-40618800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
34	chr15:40616600-40617200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
35	chr15:40616600-40617200	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:40616600-40617200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr15:40616600-40617200	Flanking Active TSS	Fetal Muscle Trunk	muscle
38	chr15:40616600-40617200	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
39	chr15:40616600-40617400	Flanking Active TSS	Primary T cells fromperipheralblood	blood
40	chr15:40616600-40617400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
41	chr15:40616600-40617600	Flanking Active TSS	Colonic Mucosa	Colon
42	chr15:40616600-40617600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr15:40616600-40617600	Flanking Active TSS	Placenta	Placenta
44	chr15:40616600-40617800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr15:40616600-40618000	Enhancers	Primary T killer memory cells from peripheral blood	blood
46	chr15:40616800-40617200	Flanking Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr15:40616800-40617200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:40616800-40617200	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
49	chr15:40616800-40617200	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
50	chr15:40616800-40617200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin

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