Variant report

Variant	rs55945670
Chromosome Location	chr15:40625758-40625759
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:40621505-40626199	U87	brain:	n/a	n/a
2	POLR2A	chr15:40621503-40626030	U87	brain:	n/a	n/a
3	POLR2A	chr15:40625755-40627147	HUVEC	blood vessel:	n/a	n/a
4	POLR2A	chr15:40621645-40626480	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr15:40621593-40626881	SK-N-MC	brain:	n/a	n/a
6	POLR2A	chr15:40625723-40626842	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40619706..40623827-chr15:40624940..40628910,6	MCF-7	breast:
2	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:
3	chr15:40625172..40629583-chr15:40631432..40633911,6	MCF-7	breast:

Variant related genes	Relation type
RNA5SP392	TF binding region
ENSG00000188549	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs11540714	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008462	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]
rs9672591	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs55945670	KNSTRN	cis	Whole Blood	GTEx
rs55945670	KNSTRN	cis	Heart Left Ventricle	GTEx
rs55945670	KNSTRN	cis	Muscle Skeletal	GTEx
rs55945670	KNSTRN	cis	Artery Tibial	GTEx
rs55945670	KNSTRN	cis	Artery Aorta	GTEx
rs55945670	IVD	Cis_1M	lymphoblastoid	RTeQTL
rs55945670	KNSTRN	cis	Esophagus Muscularis	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40617200-40630200	Weak transcription	A549	lung
2	chr15:40617400-40626000	Weak transcription	Liver	Liver
3	chr15:40617400-40626000	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:40617400-40626400	Weak transcription	Pancreas	Pancrea
5	chr15:40617400-40627000	Weak transcription	Gastric	stomach
6	chr15:40618000-40625800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
7	chr15:40618000-40625800	Weak transcription	Dnd41	blood
8	chr15:40618200-40625800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr15:40618200-40626000	Weak transcription	Stomach Mucosa	stomach
10	chr15:40618400-40625800	Weak transcription	Primary B cells from peripheral blood	blood
11	chr15:40618400-40625800	Weak transcription	Esophagus	oesophagus
12	chr15:40618400-40626800	Weak transcription	Small Intestine	intestine
13	chr15:40618400-40628200	Weak transcription	Brain Germinal Matrix	brain
14	chr15:40619400-40627400	Enhancers	Placenta	Placenta
15	chr15:40619600-40630400	Enhancers	Primary hematopoietic stem cells	blood
16	chr15:40620000-40626000	Enhancers	Rectal Smooth Muscle	rectum
17	chr15:40620000-40627800	Enhancers	Left Ventricle	heart
18	chr15:40620400-40628200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:40620800-40626000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:40620800-40629600	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr15:40621000-40626000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr15:40621000-40626000	Enhancers	Colon Smooth Muscle	Colon
23	chr15:40621000-40627000	Enhancers	HSMMtube	muscle
24	chr15:40621000-40630200	Weak transcription	HepG2	liver
25	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
26	chr15:40621200-40625800	Weak transcription	Thymus	Thymus
27	chr15:40621200-40626200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:40621200-40626200	Weak transcription	Fetal Brain Female	brain
29	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
30	chr15:40621400-40625800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr15:40621400-40626000	Weak transcription	HUES6 Cell Line	embryonic stem cell
32	chr15:40621400-40626000	Weak transcription	NHEK	skin
33	chr15:40621400-40626400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40621400-40627000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:40621400-40629800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:40621600-40626400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr15:40621600-40626600	Enhancers	Right Ventricle	heart
38	chr15:40621800-40625800	Enhancers	Primary monocytes fromperipheralblood	blood
39	chr15:40621800-40626000	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:40621800-40626800	Enhancers	Lung	lung
41	chr15:40621800-40627000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr15:40622400-40633800	Enhancers	Spleen	Spleen
43	chr15:40622600-40625800	Weak transcription	Osteobl	bone
44	chr15:40622800-40626000	Weak transcription	NH-A	brain
45	chr15:40622800-40626200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr15:40622800-40626200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr15:40622800-40628400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr15:40623000-40625800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:40623000-40625800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:40623000-40625800	Weak transcription	Fetal Intestine Large	intestine

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