Variant report

Variant	rs2325748
Chromosome Location	chr17:45974251-45974252
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	ELF1	chr17:45973012-45974262	K562	blood:	n/a	chr17:45973616-45973625 chr17:45973917-45973926 chr17:45973717-45973729 chr17:45973739-45973751 chr17:45973922-45973934 chr17:45973672-45973681 chr17:45973858-45973869 chr17:45973617-45973629
2	CREB1	chr17:45972563-45974441	HepG2	liver:	n/a	n/a
3	POLR2A	chr17:45973403-45974413	GM12891	blood:	n/a	n/a
4	SIN3AK20	chr17:45972607-45974414	PANC-1	pancreas:	n/a	n/a
5	GABPA	chr17:45972575-45974516	A549	lung:	n/a	chr17:45973881-45973890
6	POLR2A	chr17:45972255-45974960	HCT-116	colon:	n/a	n/a
7	POLR2A	chr17:45972099-45974517	GM12878	blood:	n/a	n/a
8	POLR2A	chr17:45972596-45974394	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr17:45972526-45974422	PANC-1	pancreas:	n/a	n/a
10	MAZ	chr17:45972534-45974451	Hela-S3	cervix:	n/a	chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
11	GABPA	chr17:45972942-45974363	Hela-S3	cervix:	n/a	chr17:45973881-45973890
12	MYC	chr17:45973490-45974276	MCF-7	breast:	n/a	chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
13	MYBL2	chr17:45972425-45974378	HepG2	liver:	n/a	n/a
14	PML	chr17:45972423-45974372	GM12878	blood:	n/a	n/a
15	GABPA	chr17:45972913-45974261	HL-60	blood:	n/a	chr17:45973881-45973890
16	POLR2A	chr17:45972626-45974373	GM18951	blood:	n/a	n/a
17	POLR2A	chr17:45972080-45974536	PBDE	blood:	n/a	n/a
18	MYC	chr17:45972394-45974284	NB4	blood:	n/a	chr17:45973375-45973385 chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
19	CHD2	chr17:45972587-45974316	Hela-S3	cervix:	n/a	chr17:45973879-45973889
20	POLR2A	chr17:45972590-45974808	MCF10A-Er-Src	breast:	n/a	n/a
21	POLR2A	chr17:45972451-45974292	GM12891	blood:	n/a	n/a
22	POLR2A	chr17:45972666-45974282	GM19193	blood:	n/a	n/a
23	POLR2A	chr17:45972487-45974415	MCF-7	breast:	n/a	n/a
24	TBP	chr17:45972171-45974290	K562	blood:	n/a	n/a
25	MAX	chr17:45973574-45974394	SK-N-SH	brain:	n/a	chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
26	SP1	chr17:45972222-45974349	A549	lung:	n/a	chr17:45973879-45973891 chr17:45973880-45973889 chr17:45973795-45973807 chr17:45973762-45973771 chr17:45973298-45973310 chr17:45973298-45973310 chr17:45973963-45973976 chr17:45973795-45973807 chr17:45973299-45973313 chr17:45973300-45973309 chr17:45973880-45973894 chr17:45973796-45973805 chr17:45973797-45973806 chr17:45973008-45973017 chr17:45973881-45973890 chr17:45973880-45973889 chr17:45973879-45973891 chr17:45973195-45973216 chr17:45973299-45973308 chr17:45973477-45973498 chr17:45973355-45973376
27	EBF1	chr17:45972923-45974372	GM12878	blood:	n/a	chr17:45974125-45974134
28	POLR2A	chr17:45972483-45974284	GM12878	blood:	n/a	n/a
29	ELF1	chr17:45972697-45974393	SK-N-SH	brain:	n/a	chr17:45973616-45973625 chr17:45973917-45973926 chr17:45973717-45973729 chr17:45973739-45973751 chr17:45973922-45973934 chr17:45973672-45973681 chr17:45973858-45973869 chr17:45973617-45973629
30	ELF1	chr17:45972809-45974425	A549	lung:	n/a	chr17:45973616-45973625 chr17:45973917-45973926 chr17:45973717-45973729 chr17:45973739-45973751 chr17:45973922-45973934 chr17:45973672-45973681 chr17:45973858-45973869 chr17:45973617-45973629
31	POLR2A	chr17:45972948-45974305	HepG2	liver:	n/a	n/a
32	POLR2A	chr17:45972422-45974316	K562	blood:	n/a	n/a
33	PBX3	chr17:45972433-45974663	SK-N-SH	brain:	n/a	chr17:45973081-45973090 chr17:45973491-45973511 chr17:45973411-45973431 chr17:45973369-45973389 chr17:45973205-45973214 chr17:45973382-45973391 chr17:45973533-45973553
34	MAX	chr17:45972549-45974299	NB4	blood:	n/a	chr17:45973375-45973385 chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
35	POLR2A	chr17:45972482-45974987	Hela-S3	cervix:	n/a	n/a
36	MAX	chr17:45972520-45974645	Hela-S3	cervix:	n/a	chr17:45973375-45973385 chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
37	SP1	chr17:45972136-45974646	HCT-116	colon:	n/a	chr17:45973879-45973891 chr17:45973880-45973889 chr17:45973795-45973807 chr17:45973762-45973771 chr17:45973298-45973310 chr17:45973298-45973310 chr17:45973963-45973976 chr17:45973795-45973807 chr17:45973299-45973313 chr17:45973300-45973309 chr17:45973880-45973894 chr17:45973796-45973805 chr17:45973797-45973806 chr17:45973008-45973017 chr17:45973881-45973890 chr17:45973880-45973889 chr17:45973879-45973891 chr17:45973195-45973216 chr17:45973299-45973308 chr17:45973477-45973498 chr17:45973355-45973376
38	POLR2A	chr17:45972696-45974697	IMR90	lung:	n/a	n/a
39	POLR2A	chr17:45973455-45974392	H1-hESC	embryonic stem cell:	n/a	n/a
40	POLR2A	chr17:45972568-45974274	GM12878	blood:	n/a	n/a
41	POLR2A	chr17:45972373-45974447	GM12892	blood:	n/a	n/a
42	SREBP1	chr17:45973020-45974276	HepG2	liver:	n/a	chr17:45973186-45973197
43	GABPA	chr17:45973033-45974271	HepG2	liver:	n/a	chr17:45973881-45973890
44	MAX	chr17:45972463-45974443	K562	blood:	n/a	chr17:45973375-45973385 chr17:45973882-45973892 chr17:45973720-45973730 chr17:45973742-45973752
45	MAFK	chr17:45973889-45974409	Hela-S3	cervix:	n/a	n/a
46	TAF1	chr17:45972691-45974364	ECC-1	luminal epithelium:	n/a	n/a
47	POLR2A	chr17:45972459-45974345	Hela-S3	cervix:	n/a	n/a
48	POLR2A	chr17:45972589-45974393	HL-60	blood:	n/a	n/a
49	POLR2A	chr17:45972402-45974608	K562	blood:	n/a	n/a
50	ELF1	chr17:45972573-45974269	MCF-7	breast:	n/a	chr17:45973616-45973625 chr17:45973917-45973926 chr17:45973717-45973729 chr17:45973739-45973751 chr17:45973922-45973934 chr17:45973672-45973681 chr17:45973858-45973869 chr17:45973617-45973629

No.	Distal block	Cell Line	Cell type
1	chr17:45939167..45942098-chr17:45971547..45974421,3	MCF-7	breast:
2	chr17:45921031..45932631-chr17:45970978..45975136,16	K562	blood:
3	chr17:45918236..45922252-chr17:45971224..45975227,6	K562	blood:
4	chr17:45959646..45962824-chr17:45972724..45975938,3	K562	blood:
5	chr17:45908246..45910427-chr17:45971152..45975040,4	K562	blood:
6	chr17:45971907..45976557-chr17:46046916..46050358,7	K562	blood:
7	chr17:45909005..45911115-chr17:45973524..45976296,3	MCF-7	breast:
8	chr17:45907865..45909742-chr17:45974096..45976119,2	MCF-7	breast:
9	chr17:45973201..45977546-chr17:46016018..46021091,7	K562	blood:
10	chr17:45973797..45976110-chr17:46092219..46094181,2	MCF-7	breast:
11	chr17:45897420..45900355-chr17:45972655..45975500,3	MCF-7	breast:
12	chr17:45908927..45910597-chr17:45972583..45974861,2	K562	blood:
13	chr17:45913357..45915949-chr17:45973586..45976163,2	K562	blood:
14	chr17:45906763..45908800-chr17:45971600..45974534,3	MCF-7	breast:
15	chr17:45895199..45899793-chr17:45971655..45976847,6	K562	blood:
16	chr17:45970912..45974701-chr17:46018890..46021752,3	K562	blood:
17	chr17:45931240..45934148-chr17:45971745..45974291,3	MCF-7	breast:
18	chr17:45973640..45975276-chr17:46101393..46103848,2	MCF-7	breast:
19	chr17:45915230..45925590-chr17:45966201..45976437,35	MCF-7	breast:
20	chr17:45969751..45975935-chr17:46032072..46038613,14	MCF-7	breast:
21	chr17:45959646..45961170-chr17:45972984..45974723,2	K562	blood:
22	chr17:45972440..45974489-chr17:46124453..46126583,3	MCF-7	breast:
23	chr17:45974031..45975859-chr17:46008200..46010414,2	MCF-7	breast:
24	chr17:45973858..45976253-chr17:46007245..46011089,3	K562	blood:
25	chr17:45971907..45974928-chr17:46046916..46050084,5	K562	blood:
26	chr17:45973395..45975502-chr17:46008931..46011121,2	MCF-7	breast:
27	chr17:45970281..45975378-chr17:46022719..46027732,11	MCF-7	breast:
28	chr17:45913484..45922782-chr17:45969196..45975741,24	MCF-7	breast:
29	chr17:45914946..45918155-chr17:45971112..45974378,4	K562	blood:
30	chr17:45971215..45974947-chr17:46046480..46050487,6	MCF-7	breast:
31	chr17:45971510..45977679-chr17:46016123..46021422,20	MCF-7	breast:
32	chr17:45968434..45977260-chr17:46017847..46029594,27	MCF-7	breast:
33	chr17:45923146..45930414-chr17:45970842..45976007,11	MCF-7	breast:
34	chr17:45973963..45975508-chr17:45999326..46001270,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000264920	TF binding region
ENSG00000108465	Chromatin interaction
ENSG00000141295	Chromatin interaction
ENSG00000006025	Chromatin interaction
ENSG00000159111	Chromatin interaction
ENSG00000141294	Chromatin interaction
ENSG00000082641	Chromatin interaction
ENSG00000266601	Chromatin interaction
ENSG00000234494	Chromatin interaction
ENSG00000264243	Chromatin interaction
ENSG00000167183	Chromatin interaction
ENSG00000263798	Chromatin interaction
ENSG00000263412	Chromatin interaction
ENSG00000189120	Chromatin interaction
ENSG00000108439	Chromatin interaction
ENSG00000266821	Chromatin interaction
ENSG00000264019	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11079800	0.82[ASW][hapmap];0.92[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.82[YRI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11079802	0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11650395	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11651753	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs11653445	0.83[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12939572	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12942207	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16949418	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16949720	0.90[JPT][hapmap]
rs2002136	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs2256020	0.82[YRI][hapmap]
rs2525095	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs2525109	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2525110	0.87[CHB][hapmap];0.81[JPT][hapmap]
rs2597169	0.91[CHB][hapmap];0.85[JPT][hapmap]
rs2875735	0.91[CHB][hapmap];0.86[JPT][hapmap]
rs3764394	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3764398	0.85[ASN][1000 genomes]
rs4794331	0.91[CHB][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap]
rs59811700	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs71377324	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7207225	0.92[CEU][hapmap];1.00[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7220104	1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap]
rs72833480	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs72833491	0.99[ASN][1000 genomes]
rs72840233	0.99[ASN][1000 genomes]
rs8066574	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8079333	0.83[EUR][1000 genomes]
rs8182261	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9899097	0.84[EUR][1000 genomes];0.98[ASN][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	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	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
3	nsv908575	chr17:45957591-46049533	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2325748	PNPO	cis	Skin Sun Exposed Lower leg	GTEx
rs2325748	VAT1	cis	cerebellum	SCAN
rs2325748	SP2	cis	lymphoblastoid	seeQTL
rs2325748	CALCOCO2	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:45971400-45974600	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr17:45971800-45974400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr17:45971800-45974400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr17:45971800-45974600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr17:45972000-45974800	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr17:45972000-45974800	Active TSS	NHDF-Ad	bronchial
7	chr17:45972200-45974400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr17:45972200-45974400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr17:45972200-45974600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr17:45972200-45974600	Active TSS	HUES48 Cell Line	embryonic stem cell
11	chr17:45972200-45974600	Active TSS	iPS-18 Cell Line	embryonic stem cell
12	chr17:45972200-45974600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
13	chr17:45972200-45974600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr17:45972200-45974600	Active TSS	Fetal Intestine Large	intestine
15	chr17:45972200-45974600	Active TSS	Ovary	ovary
16	chr17:45972200-45974600	Active TSS	Stomach Mucosa	stomach
17	chr17:45972200-45974800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
18	chr17:45972200-45974800	Active TSS	H1 Cell Line	embryonic stem cell
19	chr17:45972200-45974800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
20	chr17:45972200-45974800	Active TSS	Right Atrium	heart
21	chr17:45972400-45974400	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr17:45972400-45974400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr17:45972400-45974400	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr17:45972400-45974400	Active TSS	Rectal Mucosa Donor 31	rectum
25	chr17:45972400-45974400	Active TSS	Small Intestine	intestine
26	chr17:45972400-45974600	Active TSS	ES-I3 Cell Line	embryonic stem cell
27	chr17:45972400-45974600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr17:45972400-45974600	Active TSS	HUES64 Cell Line	embryonic stem cell
29	chr17:45972400-45974600	Active TSS	iPS-15b Cell Line	embryonic stem cell
30	chr17:45972400-45974600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
31	chr17:45972400-45974600	Active TSS	Esophagus	oesophagus
32	chr17:45972400-45974600	Active TSS	Fetal Kidney	kidney
33	chr17:45972400-45974600	Active TSS	Lung	lung
34	chr17:45972400-45974600	Active TSS	Pancreas	Pancrea
35	chr17:45972400-45974600	Active TSS	NHLF	lung
36	chr17:45972400-45974800	Active TSS	H9 Cell Line	embryonic stem cell
37	chr17:45972400-45974800	Active TSS	Aorta	Aorta
38	chr17:45972400-45974800	Active TSS	Left Ventricle	heart
39	chr17:45972400-45974800	Active TSS	Psoas Muscle	Psoas
40	chr17:45972400-45974800	Active TSS	Right Ventricle	heart
41	chr17:45972400-45974800	Active TSS	GM12878-XiMat	blood
42	chr17:45972400-45975000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
43	chr17:45972400-45975000	Active TSS	Fetal Muscle Trunk	muscle
44	chr17:45972600-45974400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr17:45972600-45974400	Active TSS	Muscle Satellite Cultured Cells	--
46	chr17:45972600-45974400	Active TSS	Brain Angular Gyrus	brain
47	chr17:45972600-45974400	Active TSS	Colon Smooth Muscle	Colon
48	chr17:45972600-45974400	Active TSS	Duodenum Mucosa	Duodenum
49	chr17:45972600-45974400	Active TSS	Fetal Brain Male	brain
50	chr17:45972600-45974400	Active TSS	Pancreatic Islets	Pancreatic Islet

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