Variant report

Variant	rs2325752
Chromosome Location	chr17:45921906-45921907
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	CTCF	chr17:45921544-45922799	A549	lung:	n/a	n/a
2	MAX	chr17:45921546-45921946	Hela-S3	cervix:	n/a	chr17:45921665-45921675 chr17:45921666-45921673
3	SIN3AK20	chr17:45921276-45922662	MCF-7	breast:	n/a	n/a
4	MYC	chr17:45921723-45921927	MCF-7	breast:	n/a	n/a
5	CCNT2	chr17:45921666-45921951	K562	blood:	n/a	n/a
6	JUND	chr17:45921622-45921973	K562	blood:	n/a	n/a
7	HDAC2	chr17:45921508-45922039	MCF-7	breast:	n/a	n/a
8	CEBPB	chr17:45921535-45921975	HepG2	liver:	n/a	chr17:45921780-45921788
9	CEBPB	chr17:45921540-45922074	Hela-S3	cervix:	n/a	chr17:45921780-45921788
10	PBX3	chr17:45921521-45922003	SK-N-SH	brain:	n/a	chr17:45921851-45921860
11	GATA1	chr17:45921384-45922579	K562	blood:	n/a	n/a
12	CEBPD	chr17:45921589-45921993	K562	blood:	n/a	n/a
13	GATA3	chr17:45921413-45922237	SK-N-SH	brain:	n/a	n/a
14	RCOR1	chr17:45921729-45921958	Hela-S3	cervix:	n/a	n/a
15	PBX3	chr17:45921549-45922060	SK-N-SH	brain:	n/a	chr17:45921851-45921860
16	TCF7L2	chr17:45921515-45922125	Hela-S3	cervix:	n/a	chr17:45921799-45921813
17	GATA3	chr17:45921472-45922242	MCF-7	breast:	n/a	n/a
18	EP300	chr17:45921659-45921935	Hela-S3	cervix:	n/a	n/a
19	GATA2	chr17:45921562-45922065	SH-SY5Y	brain:	n/a	n/a
20	RCOR1	chr17:45921653-45921980	K562	blood:	n/a	n/a
21	CTCF	chr17:45920328-45923018	SK-N-SH	brain:	n/a	chr17:45921416-45921437 chr17:45921417-45921426
22	CEBPB	chr17:45921445-45922125	MCF-7	breast:	n/a	chr17:45921780-45921788
23	CTCF	chr17:45921900-45922050	HVMF	connective:	n/a	n/a
24	MXI1	chr17:45921473-45922139	IMR90	lung:	n/a	chr17:45921666-45921675
25	EP300	chr17:45921722-45921942	SK-N-SH_RA	brain:	n/a	n/a
26	USF2	chr17:45921639-45921935	Hela-S3	cervix:	n/a	n/a
27	GATA3	chr17:45921565-45922034	SH-SY5Y	brain:	n/a	n/a
28	GATA3	chr17:45921621-45921990	T-47D	breast:	n/a	n/a
29	POLR2A	chr17:45921449-45922779	K562	blood:	n/a	n/a
30	CTCF	chr17:45921900-45922050	HepG2	liver:	n/a	n/a
31	ZNF263	chr17:45921734-45922468	HEK293-T-REx	kidney:	n/a	chr17:45922318-45922339 chr17:45922269-45922290
32	TCF7L2	chr17:45921453-45922197	MCF-7	breast:	n/a	chr17:45921799-45921813
33	EP300	chr17:45921637-45921988	K562	blood:	n/a	n/a
34	GATA3	chr17:45921541-45921951	T-47D	breast:	n/a	n/a
35	CEBPB	chr17:45921620-45921933	K562	blood:	n/a	chr17:45921780-45921788
36	MYC	chr17:45921582-45921919	K562	blood:	n/a	chr17:45921665-45921675 chr17:45921666-45921673
37	CTCF	chr17:45921820-45921970	HPF	lung:	n/a	n/a
38	SMC3	chr17:45921681-45921975	Hela-S3	cervix:	n/a	n/a
39	ZMIZ1	chr17:45921652-45921990	K562	blood:	n/a	n/a
40	RAD21	chr17:45921688-45921926	Hela-S3	cervix:	n/a	n/a
41	JUN	chr17:45921288-45922036	K562	blood:	n/a	chr17:45921482-45921491
42	CTCF	chr17:45921880-45922030	HCM	heart:	n/a	n/a
43	MAZ	chr17:45921615-45922011	K562	blood:	n/a	chr17:45921665-45921675 chr17:45921666-45921673
44	TCF7L2	chr17:45921608-45922057	Hela-S3	cervix:	n/a	chr17:45921799-45921813
45	CEBPB	chr17:45921516-45921990	IMR90	lung:	n/a	chr17:45921780-45921788
46	GATA3	chr17:45921577-45922153	MCF-7	breast:	n/a	n/a
47	GATA3	chr17:45921365-45922300	MCF-7	breast:	n/a	n/a
48	RAD21	chr17:45920199-45922636	SK-N-SH	brain:	n/a	chr17:45921047-45921057
49	BHLHE40	chr17:45921548-45921935	K562	blood:	n/a	n/a
50	TEAD4	chr17:45921503-45921957	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr17:45920176..45925286-chr17:46018429..46022644,7	MCF-7	breast:
2	chr17:45920242..45924382-chr17:45959879..45966158,9	MCF-7	breast:
3	chr17:45902742..45905383-chr17:45921555..45923450,2	MCF-7	breast:
4	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
5	chr17:45921830..45924511-chr17:46124880..46127547,2	MCF-7	breast:
6	chr17:45921785..45923529-chr17:45941412..45943127,2	K562	blood:
7	chr17:45918850..45921918-chr17:45964837..45968341,4	K562	blood:
8	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
9	chr17:45919921..45922804-chr17:45938176..45940805,2	MCF-7	breast:
10	chr17:45920864..45922757-chr17:46000499..46002705,2	K562	blood:
11	chr17:45920681..45922665-chr17:46015895..46018695,2	K562	blood:
12	chr17:45896657..45898733-chr17:45920717..45922306,2	MCF-7	breast:
13	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
14	chr17:45921348..45922971-chr17:45966998..45967914,11	MCF-7	breast:
15	chr17:45906340..45909429-chr17:45918735..45922764,3	K562	blood:
16	chr17:45920976..45922650-chr17:45981473..45983982,2	MCF-7	breast:
17	chr17:45914114..45922201-chr17:45959661..45964608,11	MCF-7	breast:
18	chr17:45895869..45898367-chr17:45920865..45923399,2	K562	blood:
19	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:

Variant related genes	Relation type
SCRN2	TF binding region
ENSG00000082641	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264920	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000167182	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs35391053	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8064380	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs878171	0.93[LWK][hapmap]

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	nsv498122	chr17:45763853-46064327	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv908573	chr17:45858487-45956073	Genic enhancers Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
3	nsv908574	chr17:45876022-45930584	Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv517880	chr17:45887951-45933341	Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	22 gene(s)	inside rSNPs	diseases
5	nsv518892	chr17:45887951-46029432	Enhancers Bivalent Enhancer Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2325752	NPEPPS	cis	cerebellum	SCAN
rs2325752	KRT33A	cis	cerebellum	SCAN
rs2325752	TMEM101	cis	cerebellum	SCAN
rs2325752	CDK5RAP3	cis	parietal	SCAN
rs2325752	SCRN2	cis	Whole Blood	GTEx
rs2325752	SCRN2	cis	lymphoblastoid	seeQTL
rs2325752	SCRN2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45918600-45922600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr17:45918800-45922400	Enhancers	Fetal Intestine Large	intestine
3	chr17:45918800-45924600	Weak transcription	Spleen	Spleen
4	chr17:45919000-45922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr17:45919000-45922200	Enhancers	Fetal Intestine Small	intestine
6	chr17:45919200-45928000	Weak transcription	Right Atrium	heart
7	chr17:45919400-45922000	Enhancers	Stomach Mucosa	stomach
8	chr17:45919800-45922000	Enhancers	Duodenum Mucosa	Duodenum
9	chr17:45920200-45922600	Enhancers	Hela-S3	cervix
10	chr17:45920200-45922600	Enhancers	HMEC	breast
11	chr17:45920200-45923200	Enhancers	Fetal Lung	lung
12	chr17:45920200-45923800	Enhancers	K562	blood
13	chr17:45920400-45922800	Enhancers	Placenta Amnion	Placenta Amnion
14	chr17:45920600-45922600	Enhancers	Osteobl	bone
15	chr17:45920800-45923400	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
16	chr17:45920800-45923800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr17:45921000-45924600	Weak transcription	Pancreas	Pancrea
18	chr17:45921000-45927200	Weak transcription	A549	lung
19	chr17:45921200-45922400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr17:45921200-45922400	Enhancers	HepG2	liver
21	chr17:45921200-45923800	Weak transcription	NHEK	skin
22	chr17:45921200-45926000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr17:45921600-45922000	Bivalent Enhancer	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr17:45921600-45922000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr17:45921600-45922200	Bivalent Enhancer	Placenta	Placenta
26	chr17:45921600-45922800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr17:45921800-45922000	Flanking Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr17:45921800-45922000	Bivalent Enhancer	H9 Cell Line	embryonic stem cell
29	chr17:45921800-45922000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:45921800-45922000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:45921800-45922800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr17:45921800-45922800	Enhancers	Lung	lung
33	chr17:45921800-45923600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr17:45921800-45923800	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
35	chr17:45921800-45924200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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