Variant report

Variant	rs56232597
Chromosome Location	chr15:40630613-40630614
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	MAZ	chr15:40629940-40633888	IMR90	lung:	n/a	chr15:40632042-40632058
2	RAD21	chr15:40630204-40630662	ECC-1	luminal epithelium:	n/a	chr15:40630419-40630438
3	CTCF	chr15:40630290-40630613	MCF-7	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
4	MYC	chr15:40630248-40630616	K562	blood:	n/a	n/a
5	CTCF	chr15:40630232-40630797	Spleen_OC	spleen:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
6	MAFK	chr15:40630588-40630631	HepG2	liver:	n/a	n/a
7	CTCF	chr15:40629943-40631259	SK-N-SH	brain:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
8	MAFF	chr15:40630535-40630629	K562	blood:	n/a	n/a
9	CTCF	chr15:40630266-40630628	K562	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
10	JUND	chr15:40630221-40630625	K562	blood:	n/a	n/a
11	MAZ	chr15:40630197-40630777	K562	blood:	n/a	n/a
12	RAD21	chr15:40630142-40630675	H1-hESC	embryonic stem cell:	n/a	chr15:40630419-40630438
13	CTCF	chr15:40630269-40630816	GM12891	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
14	POLR2A	chr15:40630272-40630678	U87	brain:	n/a	n/a
15	POLR2A	chr15:40630262-40630771	ECC-1	luminal epithelium:	n/a	n/a
16	CTCF	chr15:40630257-40630917	GM12892	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
17	CTCF	chr15:40630279-40630729	NHEK	skin:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
18	POLR2A	chr15:40630212-40633443	IMR90	lung:	n/a	n/a
19	MAZ	chr15:40630197-40630643	GM12878	blood:	n/a	n/a
20	MYC	chr15:40630544-40630735	H1-hESC	embryonic stem cell:	n/a	n/a
21	CTCF	chr15:40630236-40630617	IMR90	lung:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
22	CTCF	chr15:40630153-40630692	MCF-7	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
23	POLR2A	chr15:40630597-40630619	ProgFib	skin:	n/a	n/a
24	RAD21	chr15:40629998-40630879	SK-N-SH	brain:	n/a	chr15:40630419-40630438
25	CTCF	chr15:40630159-40630705	K562	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
26	CTCF	chr15:40630258-40631079	GM19238	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
27	CTCF	chr15:40630049-40630768	HCT-116	colon:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
28	CTCF	chr15:40630193-40630614	H1-hESC	embryonic stem cell:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
29	ZBTB7A	chr15:40630170-40631708	ECC-1	luminal epithelium:	n/a	n/a
30	ZBTB7A	chr15:40630114-40630902	K562	blood:	n/a	n/a
31	TEAD4	chr15:40630182-40630630	K562	blood:	n/a	n/a
32	MAZ	chr15:40630265-40630680	HepG2	liver:	n/a	n/a
33	CTCF	chr15:40630286-40630627	GM10266	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
34	CTCF	chr15:40630184-40630638	HepG2	liver:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
35	FOXA2	chr15:40630234-40630727	A549	lung:	n/a	n/a
36	ZBTB7A	chr15:40630110-40633237	ECC-1	luminal epithelium:	n/a	n/a
37	RAD21	chr15:40630210-40630837	HCT-116	colon:	n/a	chr15:40630419-40630438
38	RAD21	chr15:40630190-40630616	H1-hESC	embryonic stem cell:	n/a	chr15:40630419-40630438
39	POLR2A	chr15:40630215-40633532	U87	brain:	n/a	n/a
40	POLR2A	chr15:40630273-40630673	HUVEC	blood vessel:	n/a	n/a
41	RAD21	chr15:40630230-40630616	Hela-S3	cervix:	n/a	chr15:40630419-40630438
42	RAD21	chr15:40630143-40630727	MCF-7	breast:	n/a	chr15:40630419-40630438
43	CTCF	chr15:40630209-40630639	K562	blood:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
44	POLR2A	chr15:40630162-40633385	PANC-1	pancreas:	n/a	n/a
45	MYC	chr15:40630223-40630637	NB4	blood:	n/a	n/a
46	SMC3	chr15:40630229-40630614	Hela-S3	cervix:	n/a	chr15:40630423-40630437
47	ZNF263	chr15:40630224-40630868	HEK293-T-REx	kidney:	n/a	chr15:40630597-40630606 chr15:40630457-40630478
48	CTCF	chr15:40630292-40630618	MCF-7	breast:	n/a	chr15:40630422-40630438 chr15:40630416-40630437 chr15:40630421-40630439
49	RAD21	chr15:40630225-40630615	HepG2	liver:	n/a	chr15:40630419-40630438
50	ZBTB7A	chr15:40630244-40630658	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:40628035..40631006-chr15:40631506..40634762,3	MCF-7	breast:
2	chr15:40583247..40584804-chr15:40630582..40632469,2	MCF-7	breast:
3	chr15:40614221..40619136-chr15:40629898..40635011,9	K562	blood:
4	chr15:40613279..40619250-chr15:40625286..40632667,13	MCF-7	breast:

Variant related genes	Relation type
C15orf52	TF binding region
ENSG00000188549	Chromatin interaction
ENSG00000137841	Chromatin interaction
ENSG00000259330	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11540714	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2008462	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55945670	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56044352	1.00[ASN][1000 genomes]
rs56289107	1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs56232597	KNSTRN	cis	Heart Left Ventricle	GTEx
rs56232597	KNSTRN	cis	Nerve Tibial	GTEx
rs56232597	KNSTRN	cis	Esophagus Muscularis	GTEx
rs56232597	KNSTRN	cis	Whole Blood	GTEx
rs56232597	KNSTRN	cis	Artery Aorta	GTEx
rs56232597	KNSTRN	cis	Muscle Skeletal	GTEx
rs56232597	KNSTRN	cis	Artery Tibial	GTEx
rs56232597	IVD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:107 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40621000-40637600	Enhancers	Fetal Heart	heart
2	chr15:40621200-40633400	Weak transcription	Fetal Kidney	kidney
3	chr15:40622400-40633800	Enhancers	Spleen	Spleen
4	chr15:40625800-40631600	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr15:40625800-40642800	Enhancers	Fetal Intestine Large	intestine
6	chr15:40626400-40631600	Enhancers	Adipose Nuclei	Adipose
7	chr15:40626600-40631800	Enhancers	Duodenum Mucosa	Duodenum
8	chr15:40626600-40633800	Enhancers	Primary monocytes fromperipheralblood	blood
9	chr15:40627000-40630800	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:40627000-40632200	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr15:40627000-40633400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40627600-40631400	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr15:40627800-40632200	Weak transcription	Small Intestine	intestine
14	chr15:40628000-40631200	Genic enhancers	Esophagus	oesophagus
15	chr15:40628600-40631000	Transcr. at gene 5' and 3'	HMEC	breast
16	chr15:40628800-40633600	Enhancers	Placenta	Placenta
17	chr15:40629000-40630800	Enhancers	HUES6 Cell Line	embryonic stem cell
18	chr15:40629000-40632000	Enhancers	Fetal Muscle Trunk	muscle
19	chr15:40629000-40632400	Enhancers	Fetal Intestine Small	intestine
20	chr15:40629200-40630800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr15:40629200-40631200	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
22	chr15:40629400-40631000	Enhancers	Left Ventricle	heart
23	chr15:40629400-40631600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr15:40629400-40633600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:40629400-40637200	Enhancers	Fetal Lung	lung
26	chr15:40629600-40632000	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr15:40629600-40632000	Enhancers	Fetal Muscle Leg	muscle
28	chr15:40629600-40633400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:40629600-40633600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:40629600-40633600	Enhancers	Ovary	ovary
31	chr15:40629800-40630800	Enhancers	iPS-15b Cell Line	embryonic stem cell
32	chr15:40629800-40630800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr15:40629800-40630800	Enhancers	Brain Cingulate Gyrus	brain
34	chr15:40629800-40631200	Flanking Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:40629800-40631400	Enhancers	Psoas Muscle	Psoas
36	chr15:40629800-40631400	Enhancers	HUVEC	blood vessel
37	chr15:40629800-40631600	Transcr. at gene 5' and 3'	NHEK	skin
38	chr15:40629800-40631800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:40629800-40631800	Flanking Active TSS	HSMM	muscle
40	chr15:40629800-40632000	Enhancers	Brain Germinal Matrix	brain
41	chr15:40629800-40632600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:40629800-40633600	Flanking Active TSS	Colonic Mucosa	Colon
43	chr15:40629800-40634000	Enhancers	Placenta Amnion	Placenta Amnion
44	chr15:40630000-40630800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr15:40630000-40630800	Enhancers	Right Ventricle	heart
46	chr15:40630000-40631000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
47	chr15:40630000-40632200	Enhancers	Fetal Stomach	stomach
48	chr15:40630000-40632200	Enhancers	Stomach Mucosa	stomach
49	chr15:40630000-40632600	Flanking Active TSS	HSMMtube	muscle
50	chr15:40630000-40633400	Enhancers	Fetal Brain Male	brain

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