Variant report

Variant	rs4713007
Chromosome Location	chr6:26537609-26537610
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	SMC3	chr6:26537448-26538490	HepG2	liver:	n/a	n/a
2	CHD2	chr6:26537462-26538819	Hela-S3	cervix:	n/a	n/a
3	TAF1	chr6:26537384-26538018	SK-N-SH	brain:	n/a	n/a
4	MYC	chr6:26537506-26538689	H1-hESC	embryonic stem cell:	n/a	chr6:26537947-26537958 chr6:26537947-26537957 chr6:26537947-26537956 chr6:26537947-26537958 chr6:26537948-26537957 chr6:26537946-26537959 chr6:26537578-26537587 chr6:26537947-26537957 chr6:26537946-26537961 chr6:26537944-26537959 chr6:26537948-26537958 chr6:26537946-26537959 chr6:26537946-26537959 chr6:26537949-26537958
5	E2F6	chr6:26537461-26537721	K562	blood:	n/a	n/a
6	CEBPB	chr6:26537492-26537982	A549	lung:	n/a	chr6:26537731-26537742
7	MYC	chr6:26537138-26538946	Hela-S3	cervix:	n/a	chr6:26537947-26537958 chr6:26537947-26537957 chr6:26537947-26537956 chr6:26537947-26537958 chr6:26537948-26537957 chr6:26537946-26537959 chr6:26537578-26537587 chr6:26537947-26537957 chr6:26537946-26537961 chr6:26537944-26537959 chr6:26537948-26537958 chr6:26537946-26537959 chr6:26537946-26537959 chr6:26537949-26537958
8	NFIC	chr6:26537393-26538763	GM12878	blood:	n/a	n/a
9	SP1	chr6:26537329-26538629	A549	lung:	n/a	chr6:26538132-26538141
10	POLR2A	chr6:26537440-26537797	GM12891	blood:	n/a	n/a
11	RELA	chr6:26537472-26538709	GM19099	blood:	n/a	n/a
12	MAX	chr6:26537260-26539012	HCT-116	colon:	n/a	chr6:26537947-26537958 chr6:26537947-26537957 chr6:26537947-26537956 chr6:26537947-26537958 chr6:26537948-26537957 chr6:26537946-26537959 chr6:26537578-26537587 chr6:26537947-26537957 chr6:26537946-26537961 chr6:26537944-26537959 chr6:26537948-26537958 chr6:26537946-26537959 chr6:26537946-26537959 chr6:26537949-26537958
13	FOSL2	chr6:26537457-26538763	MCF-7	breast:	n/a	n/a
14	BRF1	chr6:26537516-26538444	K562	blood:	n/a	n/a
15	POLR2A	chr6:26537338-26538935	GM12892	blood:	n/a	n/a
16	CEBPB	chr6:26537506-26537993	K562	blood:	n/a	chr6:26537731-26537742
17	MYC	chr6:26536889-26538900	NB4	blood:	n/a	chr6:26537947-26537958 chr6:26537947-26537957 chr6:26537947-26537956 chr6:26537947-26537958 chr6:26537948-26537957 chr6:26537946-26537959 chr6:26537578-26537587 chr6:26537947-26537957 chr6:26537946-26537961 chr6:26537944-26537959 chr6:26537948-26537958 chr6:26537946-26537959 chr6:26537946-26537959 chr6:26537949-26537958
18	ETS1	chr6:26537524-26538021	K562	blood:	n/a	n/a
19	TEAD4	chr6:26537512-26538614	A549	lung:	n/a	n/a
20	NFATC1	chr6:26537154-26538681	GM12878	blood:	n/a	n/a
21	E2F4	chr6:26537423-26539247	K562	blood:	n/a	chr6:26539037-26539046 chr6:26538826-26538836
22	NR2F2	chr6:26537231-26538793	K562	blood:	n/a	n/a
23	RAD21	chr6:26537378-26538511	A549	lung:	n/a	n/a
24	ZC3H11A	chr6:26537479-26538459	K562	blood:	n/a	n/a
25	MBD4	chr6:26537292-26538789	HepG2	liver:	n/a	n/a
26	E2F6	chr6:26537484-26539130	K562	blood:	n/a	chr6:26539037-26539046 chr6:26538694-26538705 chr6:26538826-26538836
27	CTCF	chr6:26537520-26537670	HCPEpiC	choroid plexus:	n/a	n/a
28	POLR2A	chr6:26537464-26538769	Hela-S3	cervix:	n/a	n/a
29	MAFK	chr6:26537077-26538384	HepG2	liver:	n/a	chr6:26537253-26537264 chr6:26537826-26537836 chr6:26537251-26537265 chr6:26537248-26537263 chr6:26537253-26537264
30	USF1	chr6:26537581-26538178	H1-hESC	embryonic stem cell:	n/a	n/a
31	CREB1	chr6:26537468-26537962	ECC-1	luminal epithelium:	n/a	n/a
32	SP4	chr6:26537245-26538761	H1-hESC	embryonic stem cell:	n/a	n/a
33	YY1	chr6:26537257-26538804	ECC-1	luminal epithelium:	n/a	chr6:26538016-26538024 chr6:26537532-26537542 chr6:26538013-26538023 chr6:26537532-26537542 chr6:26537532-26537554
34	SP1	chr6:26537379-26538690	A549	lung:	n/a	chr6:26538132-26538141
35	ELF1	chr6:26537415-26538907	GM12878	blood:	n/a	chr6:26538561-26538570
36	ZNF263	chr6:26536934-26539705	HEK293-T-REx	kidney:	n/a	chr6:26539121-26539130
37	CEBPB	chr6:26537439-26538074	HepG2	liver:	n/a	chr6:26537731-26537742
38	BCLAF1	chr6:26537011-26538795	K562	blood:	n/a	n/a
39	PML	chr6:26537229-26538830	K562	blood:	n/a	n/a
40	TAF1	chr6:26537459-26538209	K562	blood:	n/a	n/a
41	POLR2A	chr6:26537316-26538979	GM12878	blood:	n/a	n/a
42	MAFK	chr6:26536925-26538460	Hela-S3	cervix:	n/a	chr6:26537253-26537264 chr6:26537826-26537836 chr6:26537251-26537265 chr6:26537248-26537263 chr6:26537253-26537264
43	RFX5	chr6:26537551-26537855	HepG2	liver:	n/a	n/a
44	GATA3	chr6:26537313-26538976	A549	lung:	n/a	n/a
45	TCF12	chr6:26537553-26538036	GM12878	blood:	n/a	n/a
46	POLR2A	chr6:26537440-26537842	Raji	blood:	n/a	n/a
47	GTF3C2	chr6:26537524-26538837	K562	blood:	n/a	n/a
48	IRF4	chr6:26537440-26538593	GM12878	blood:	n/a	n/a
49	MAX	chr6:26537335-26538843	MCF-7	breast:	n/a	chr6:26537947-26537958 chr6:26537947-26537957 chr6:26537947-26537956 chr6:26537947-26537958 chr6:26537948-26537957 chr6:26537946-26537959 chr6:26537578-26537587 chr6:26537947-26537957 chr6:26537946-26537961 chr6:26537944-26537959 chr6:26537948-26537958 chr6:26537946-26537959 chr6:26537946-26537959 chr6:26537949-26537958
50	GATA2	chr6:26537513-26538680	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr6:26217037..26219945-chr6:26536626..26539021,2	K562	blood:
2	chr6:26536432..26537991-chr6:26565891..26568258,2	K562	blood:
3	chr6:26273305..26276123-chr6:26535998..26538001,3	K562	blood:
4	chr6:26055721..26057266-chr6:26535501..26538062,2	K562	blood:
5	chr6:26156308..26158210-chr6:26536750..26538404,2	MCF-7	breast:
6	chr6:26198554..26200175-chr6:26536662..26538943,2	K562	blood:
7	chr6:26536187..26538587-chr6:26584341..26585867,2	K562	blood:
8	chr6:26527195..26529181-chr6:26536100..26538613,2	MCF-7	breast:
9	chr6:26249452..26251500-chr6:26536200..26539102,2	K562	blood:
10	chr6:26537451..26540482-chr6:27099233..27102260,3	K562	blood:
11	chr6:26536235..26538263-chr6:27099083..27100611,2	K562	blood:
12	chr2:97534713..97536438-chr6:26537054..26540026,2	MCF-7	breast:
13	chr6:26156242..26159105-chr6:26536923..26540101,4	K562	blood:
14	chr6:26520627..26522671-chr6:26536742..26539578,4	MCF-7	breast:
15	chr6:26535400..26541597-chr6:26593643..26598951,8	K562	blood:
16	chr6:26223757..26226202-chr6:26537228..26539422,2	MCF-7	breast:
17	chr6:26156242..26159092-chr6:26536120..26538666,4	K562	blood:
18	chr1:41327548..41328470-chr6:26537446..26538135,2	Hela-S3	cervix:
19	chr6:26536174..26539515-chr6:26593643..26598624,4	K562	blood:
20	chr6:26530090..26531605-chr6:26535958..26538607,2	MCF-7	breast:
21	chr6:26537484..26538187-chr9:139137262..139137764,2	Hela-S3	cervix:
22	chr6:26156110..26158318-chr6:26536983..26539384,2	MCF-7	breast:
23	chr6:26520458..26524632-chr6:26536427..26540091,8	MCF-7	breast:

Variant related genes	Relation type
HMGN4	TF binding region
ENSG00000196866	Chromatin interaction
ENSG00000168298	Chromatin interaction
ENSG00000168274	Chromatin interaction
ENSG00000228223	Chromatin interaction
ENSG00000261353	Chromatin interaction
ENSG00000187837	Chromatin interaction
ENSG00000197846	Chromatin interaction
ENSG00000158373	Chromatin interaction
ENSG00000179862	Chromatin interaction
ENSG00000165661	Chromatin interaction
ENSG00000196787	Chromatin interaction
ENSG00000197409	Chromatin interaction
ENSG00000124635	Chromatin interaction
ENSG00000256316	Chromatin interaction
ENSG00000196966	Chromatin interaction
ENSG00000146109	Chromatin interaction
ENSG00000168758	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1535278	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];0.90[TSI][hapmap];1.00[YRI][hapmap];0.93[AMR][1000 genomes]
rs15580	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1796524	1.00[CEU][hapmap];0.91[YRI][hapmap];0.86[AMR][1000 genomes]
rs2145319	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2224379	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3736780	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3864291	1.00[JPT][hapmap]
rs6905163	0.83[AFR][1000 genomes];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6911330	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6922256	0.83[LWK][hapmap]
rs6927012	1.00[CEU][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes]
rs6929908	0.87[LWK][hapmap];1.00[MKK][hapmap]
rs7745632	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs9295697	0.95[EUR][1000 genomes]
rs9366661	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9379892	0.87[MKK][hapmap]

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	nsv1029920	chr6:25638507-26585842	Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Enhancers Weak transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
2	nsv538162	chr6:25638507-26585842	Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	1215 gene(s)	inside rSNPs	diseases
3	nsv482407	chr6:26369320-26550148	Active TSS Strong transcription Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs4713007	ZSCAN23	cis	cerebellum	SCAN
rs4713007	RP11-457M11.5	cis	Adipose Subcutaneous	GTEx
rs4713007	HIST1H3E	cis	parietal	SCAN
rs4713007	RP11-457M11.5	cis	Thyroid	GTEx
rs4713007	RP11-457M11.5	cis	Artery Aorta	GTEx
rs4713007	RP11-457M11.5	cis	lung	GTEx
rs4713007	RP11-457M11.5	cis	Esophagus Mucosa	GTEx
rs4713007	ABT1	cis	cerebellum	SCAN
rs4713007	HMGN4	cis	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:26536400-26537800	Flanking Active TSS	Adipose Nuclei	Adipose
2	chr6:26536400-26537800	Active TSS	Brain Germinal Matrix	brain
3	chr6:26536400-26538200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
4	chr6:26536400-26539200	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:26536400-26540000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:26536400-26540400	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr6:26536600-26538000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr6:26536600-26539000	Active TSS	Brain Angular Gyrus	brain
9	chr6:26536600-26539200	Active TSS	HUES6 Cell Line	embryonic stem cell
10	chr6:26536600-26539200	Active TSS	Fetal Stomach	stomach
11	chr6:26536600-26539600	Active TSS	ES-I3 Cell Line	embryonic stem cell
12	chr6:26536800-26537800	Flanking Active TSS	Primary B cells from cord blood	blood
13	chr6:26536800-26537800	Flanking Active TSS	Duodenum Mucosa	Duodenum
14	chr6:26536800-26537800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
15	chr6:26536800-26538200	Flanking Active TSS	HUVEC	blood vessel
16	chr6:26536800-26539000	Active TSS	Colonic Mucosa	Colon
17	chr6:26536800-26539400	Active TSS	Lung	lung
18	chr6:26536800-26539400	Active TSS	Right Atrium	heart
19	chr6:26536800-26539400	Active TSS	Right Ventricle	heart
20	chr6:26536800-26539600	Active TSS	H9 Cell Line	embryonic stem cell
21	chr6:26536800-26539600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr6:26536800-26539600	Active TSS	Aorta	Aorta
23	chr6:26536800-26539600	Active TSS	Psoas Muscle	Psoas
24	chr6:26536800-26540000	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr6:26536800-26540000	Active TSS	iPS-20b Cell Line	embryonic stem cell
26	chr6:26537000-26538000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
27	chr6:26537000-26538000	Flanking Active TSS	Liver	Liver
28	chr6:26537000-26538200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
29	chr6:26537000-26539000	Active TSS	Brain Cingulate Gyrus	brain
30	chr6:26537000-26539200	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr6:26537000-26539400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr6:26537000-26539400	Active TSS	iPS-18 Cell Line	embryonic stem cell
33	chr6:26537000-26539400	Active TSS	Breast Myoepithelial Primary Cells	Breast
34	chr6:26537000-26539400	Active TSS	Ovary	ovary
35	chr6:26537000-26539400	Active TSS	Small Intestine	intestine
36	chr6:26537000-26539400	Bivalent/Poised TSS	HepG2	liver
37	chr6:26537000-26539600	Active TSS	H1 Cell Line	embryonic stem cell
38	chr6:26537000-26539600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
39	chr6:26537000-26539600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
40	chr6:26537000-26539600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
41	chr6:26537000-26539600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
42	chr6:26537000-26539800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr6:26537000-26539800	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr6:26537000-26540000	Active TSS	iPS-15b Cell Line	embryonic stem cell
45	chr6:26537000-26540200	Active TSS	A549	lung
46	chr6:26537200-26539000	Active TSS	Brain Anterior Caudate	brain
47	chr6:26537200-26539000	Active TSS	Fetal Brain Male	brain
48	chr6:26537200-26539000	Active TSS	Fetal Lung	lung
49	chr6:26537200-26539200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
50	chr6:26537200-26539200	Active TSS	Duodenum Smooth Muscle	Duodenum

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