Variant report

Variant	rs6695407
Chromosome Location	chr1:154928707-154928708
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	chr1:154928290-154930403	GM12892	blood:	n/a	n/a
2	POLR2A	chr1:154928221-154929510	HL-60	blood:	n/a	n/a
3	USF1	chr1:154928245-154929131	HCT-116	colon:	n/a	chr1:154928617-154928628
4	POLR2A	chr1:154928664-154928790	A549	lung:	n/a	n/a
5	MAX	chr1:154928296-154928770	SK-N-SH	brain:	n/a	chr1:154928618-154928627 chr1:154928616-154928629
6	TAF1	chr1:154928189-154928908	H1-hESC	embryonic stem cell:	n/a	n/a
7	MAZ	chr1:154927684-154928928	GM12878	blood:	n/a	chr1:154928618-154928627 chr1:154927881-154927890 chr1:154928616-154928629 chr1:154927850-154927859 chr1:154927885-154927894
8	SP1	chr1:154928356-154928897	K562	blood:	n/a	chr1:154928634-154928655 chr1:154928422-154928436 chr1:154928705-154928714 chr1:154928676-154928697 chr1:154928704-154928715
9	USF1	chr1:154928455-154928788	HepG2	liver:	n/a	chr1:154928617-154928628
10	USF1	chr1:154928287-154928863	A549	lung:	n/a	chr1:154928617-154928628
11	SP2	chr1:154928384-154928834	HepG2	liver:	n/a	chr1:154928678-154928688 chr1:154928657-154928672 chr1:154928636-154928646
12	HEY1	chr1:154928268-154929027	HepG2	liver:	n/a	n/a
13	POLR2A	chr1:154928064-154928874	Hela-S3	cervix:	n/a	n/a
14	POLR2A	chr1:154927217-154931608	K562	blood:	n/a	n/a
15	POLR2A	chr1:154927962-154928881	A549	lung:	n/a	n/a
16	TBL1XR1	chr1:154928375-154928865	GM12878	blood:	n/a	n/a
17	SP4	chr1:154928240-154928901	H1-hESC	embryonic stem cell:	n/a	chr1:154928657-154928673 chr1:154928704-154928715
18	CTCF	chr1:154928640-154928790	HMF	breast:	n/a	chr1:154928653-154928671 chr1:154928656-154928669 chr1:154928754-154928763
19	POLR2A	chr1:154928650-154928835	ProgFib	skin:	n/a	n/a
20	POLR2A	chr1:154927351-154929991	GM12878	blood:	n/a	n/a
21	CHD2	chr1:154928189-154929479	Hela-S3	cervix:	n/a	n/a
22	POLR2A	chr1:154927438-154929998	GM12878	blood:	n/a	n/a
23	MAFK	chr1:154928339-154928818	HepG2	liver:	n/a	n/a
24	USF1	chr1:154928217-154928956	A549	lung:	n/a	chr1:154928617-154928628
25	POLR2A	chr1:154928338-154929006	HCT-116	colon:	n/a	n/a
26	CTCF	chr1:154928700-154928850	GM06990	blood:	n/a	chr1:154928754-154928763
27	RFX5	chr1:154928376-154928792	GM12878	blood:	n/a	n/a
28	POLR2A	chr1:154927565-154929025	IMR90	lung:	n/a	n/a
29	USF1	chr1:154928315-154928886	A549	lung:	n/a	chr1:154928617-154928628
30	POLR2A	chr1:154928641-154928939	MCF-7	breast:	n/a	n/a
31	POLR2A	chr1:154927233-154929589	HepG2	liver:	n/a	n/a
32	USF1	chr1:154928212-154929212	HCT-116	colon:	n/a	chr1:154928617-154928628
33	CTCF	chr1:154928700-154928850	SAEC	small airway:	n/a	chr1:154928754-154928763
34	POLR2A	chr1:154928224-154929586	HUVEC	blood vessel:	n/a	n/a
35	POLR2A	chr1:154928265-154928979	NB4	blood:	n/a	n/a
36	POLR2A	chr1:154928206-154928862	H1-hESC	embryonic stem cell:	n/a	n/a
37	USF1	chr1:154928315-154928879	A549	lung:	n/a	chr1:154928617-154928628
38	POLR2A	chr1:154928253-154930927	PANC-1	pancreas:	n/a	n/a
39	POLR2A	chr1:154928594-154929000	A549	lung:	n/a	n/a
40	NFYB	chr1:154928366-154928887	K562	blood:	n/a	chr1:154928675-154928690 chr1:154928630-154928645 chr1:154928672-154928687 chr1:154928632-154928644 chr1:154928675-154928689 chr1:154928633-154928647 chr1:154928675-154928690
41	SPI1	chr1:154928012-154928921	HL-60	blood:	n/a	chr1:154928157-154928170 chr1:154928706-154928719 chr1:154928391-154928400 chr1:154928231-154928244
42	IRF3	chr1:154928519-154928782	GM12878	blood:	n/a	chr1:154928625-154928636
43	POLR2A	chr1:154928463-154929001	K562	blood:	n/a	n/a
44	ZBTB7A	chr1:154928639-154929029	K562	blood:	n/a	n/a
45	GTF2F1	chr1:154928107-154928829	Hela-S3	cervix:	n/a	n/a
46	POLR2A	chr1:154927411-154929816	GM12891	blood:	n/a	n/a
47	TBP	chr1:154927670-154928810	H1-hESC	embryonic stem cell:	n/a	n/a
48	RUNX3	chr1:154927337-154929034	GM12878	blood:	n/a	n/a
49	CTCF	chr1:154928600-154928750	AG04450	lung:	n/a	chr1:154928653-154928671 chr1:154928656-154928669
50	MAX	chr1:154928341-154928876	HepG2	liver:	n/a	chr1:154928618-154928627 chr1:154928616-154928629

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:154928667-154928717	HCF	heart:	n/a
2	chr1:154928667-154928717	HPAEpiC	pulmonary alveolar:	n/a
3	chr1:154928667-154928717	MCF-7	breast:	n/a
4	chr1:154928667-154928717	HRCEpiC	kidney:	n/a
5	chr1:154928667-154928717	IMR90	lung:	fetal
6	chr1:154928667-154928717	AG09309	skin:	n/a
7	chr1:154928667-154928717	HIPEpiC	eye:	n/a
8	chr1:154928667-154928717	CMK	blood:	n/a
9	chr1:154928667-154928717	BE2_C	brain:	n/a
10	chr1:154928667-154928717	NHDF-neo	bronchial:	n/a
11	chr1:154928667-154928717	HCM	heart:	n/a
12	chr1:154928667-154928717	PrEC	prostate:	n/a
13	chr1:154928667-154928717	PANC-1	pancreas:	n/a
14	chr1:154928667-154928717	U87	brain:	n/a
15	chr1:154928667-154928717	HL-60	blood:	n/a
16	chr1:154928667-154928717	HEEpiC	esophagus:	n/a
17	chr1:154928667-154928717	A549	lung:	n/a
18	chr1:154928667-154928717	GM12892	blood:	n/a
19	chr1:154928667-154928717	HNPCEpiC	eye:	n/a
20	chr1:154928667-154928717	LNCaP	prostate:	n/a
21	chr1:154928667-154928717	AG10803	skin:	n/a
22	chr1:154928667-154928717	RPTEC	kidney:	n/a
23	chr1:154928667-154928717	SKMC	muscle:	n/a
24	chr1:154928667-154928717	NHBE	bronchial:	n/a
25	chr1:154928667-154928717	SK-N-SH	brain:	n/a
26	chr1:154928667-154928717	HEK293	kidney:	embryo
27	chr1:154928667-154928717	ovcar-3	ovarian:	n/a
28	chr1:154928667-154928717	K562	blood:	n/a
29	chr1:154928667-154928717	AG04450	lung:	fetal
30	chr1:154928667-154928717	T-47D	breast:	n/a
31	chr1:154928667-154928717	NT2-D1	testis:	n/a
32	chr1:154928667-154928717	AG04449	skin:	fetal
33	chr1:154928667-154928717	HepG2	liver:	n/a
34	chr1:154928667-154928717	HRPEpiC	eye:	n/a
35	chr1:154928667-154928717	BJ	skin:	n/a
36	chr1:154928667-154928717	MCF10A-Er-Src	breast:	n/a
37	chr1:154928667-154928717	PFSK-1	brain:	n/a
38	chr1:154928667-154928717	AoSMC	blood vessel:	n/a
39	chr1:154928667-154928717	SK-N-SH_RA	brain:	n/a
40	chr1:154928667-154928717	ECC-1	luminal epithelium:	n/a
41	chr1:154928667-154928717	AG09319	gingival:	n/a
42	chr1:154928667-154928717	Caco-2	colon:	n/a
43	chr1:154928667-154928717	SAEC	small airway:	n/a
44	chr1:154928667-154928717	HMEC	breast:	n/a
45	chr1:154928667-154928717	HCT-116	colon:	n/a
46	chr1:154928667-154928717	HCPEpiC	choroid plexus:	n/a
47	chr1:154928667-154928717	GM06990	blood:	n/a
48	chr1:154928667-154928717	H1-hESC	embryonic stem cell:	embryo
49	chr1:154928667-154928717	HAEpiC	amniotic membrane:	n/a
50	chr1:154928667-154928717	NB4	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:154903245..154906216-chr1:154928700..154931455,2	K562	blood:
2	chr1:154927971..154930365-chr17:56736416..56738010,2	MCF-7	breast:
3	chr1:154927402..154930292-chr1:155021901..155025717,6	MCF-7	breast:
4	chr1:154927595..154930613-chr1:155023082..155024913,3	K562	blood:
5	chr1:154927691..154930617-chr1:155023229..155025423,2	MCF-7	breast:
6	chr1:154927481..154932587-chr1:155031885..155037682,6	MCF-7	breast:
7	chr1:154927921..154930656-chr1:155100547..155102182,2	MCF-7	breast:
8	chr1:154928213..154928938-chr1:154946568..154947462,2	K562	blood:

Variant related genes	Relation type
PBXIP1	TF binding region
PBXIP1	CpG island
ENSG00000243364	Chromatin interaction
ENSG00000169242	Chromatin interaction
ENSG00000160691	Chromatin interaction
ENSG00000251246	Chromatin interaction
ENSG00000202077	Chromatin interaction
ENSG00000173207	Chromatin interaction
ENSG00000143537	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10908449	1.00[CHD][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11264293	1.00[CHD][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1131397	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585145	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11587981	1.00[ASN][1000 genomes]
rs12075984	1.00[CHD][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076073	1.00[CHD][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12096640	1.00[ASN][1000 genomes]
rs16836580	1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16836586	1.00[YRI][hapmap]
rs2089247	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs2089248	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs2878517	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[ASN][1000 genomes]
rs28851228	1.00[ASN][1000 genomes]
rs3766921	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59519769	1.00[ASN][1000 genomes]
rs6661212	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6671228	0.85[YRI][hapmap]
rs6683093	1.00[ASN][1000 genomes]
rs6696397	1.00[CHD][hapmap];1.00[MEX][hapmap];1.00[ASN][1000 genomes]
rs7525164	1.00[ASN][1000 genomes]
rs7525580	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7528060	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs7528548	0.84[ASW][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap];0.85[YRI][hapmap];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs7535144	1.00[ASN][1000 genomes]
rs7549705	1.00[YRI][hapmap]
rs8191979	1.00[CHD][hapmap];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532579	chr1:154548165-155262692	Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	575 gene(s)	inside rSNPs	diseases
2	nsv427797	chr1:154559115-154933717	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv872453	chr1:154904840-154995503	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
4	nsv872454	chr1:154904840-155079477	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	181 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:154924200-154929200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
2	chr1:154924400-154929400	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
3	chr1:154925000-154929200	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr1:154925200-154930000	Flanking Active TSS	Stomach Smooth Muscle	stomach
5	chr1:154926200-154929400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
6	chr1:154926200-154929400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr1:154926200-154929400	Flanking Active TSS	Dnd41	blood
8	chr1:154926200-154929600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr1:154927000-154929400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr1:154927000-154929400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
11	chr1:154927000-154929400	Flanking Active TSS	Brain Anterior Caudate	brain
12	chr1:154927200-154929000	Flanking Active TSS	Fetal Brain Male	brain
13	chr1:154927200-154929200	Flanking Active TSS	Primary B cells from cord blood	blood
14	chr1:154927200-154929200	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
15	chr1:154927200-154929400	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
16	chr1:154927200-154929600	Flanking Active TSS	Adipose Nuclei	Adipose
17	chr1:154927200-154929800	Flanking Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
18	chr1:154927400-154929000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr1:154927400-154929200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr1:154927400-154929400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr1:154927400-154929400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
22	chr1:154927600-154928800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
23	chr1:154927600-154928800	Active TSS	Primary T helper naive cells fromperipheralblood	blood
24	chr1:154927600-154928800	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:154927600-154928800	Active TSS	Primary T killer naive cells fromperipheralblood	blood
26	chr1:154927600-154928800	Active TSS	Primary T killer memory cells from peripheral blood	blood
27	chr1:154927600-154929000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
28	chr1:154927600-154929000	Active TSS	Primary T helper naive cells from peripheral blood	blood
29	chr1:154927600-154929400	Flanking Active TSS	Liver	Liver
30	chr1:154927800-154928800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr1:154927800-154928800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr1:154927800-154928800	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr1:154927800-154928800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr1:154927800-154929000	Active TSS	HUES6 Cell Line	embryonic stem cell
35	chr1:154927800-154929000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr1:154927800-154929000	Active TSS	Colon Smooth Muscle	Colon
37	chr1:154927800-154929000	Active TSS	Pancreas	Pancrea
38	chr1:154927800-154929000	Active TSS	Sigmoid Colon	Sigmoid Colon
39	chr1:154927800-154929000	Active TSS	A549	lung
40	chr1:154927800-154929000	Active TSS	HSMMtube	muscle
41	chr1:154927800-154929200	Active TSS	Aorta	Aorta
42	chr1:154927800-154929200	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
43	chr1:154927800-154929200	Active TSS	Gastric	stomach
44	chr1:154927800-154929400	Active TSS	H9 Cell Line	embryonic stem cell
45	chr1:154927800-154929400	Flanking Active TSS	HUVEC	blood vessel
46	chr1:154927800-154929400	Flanking Active TSS	NHEK	skin
47	chr1:154928000-154928800	Active TSS	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr1:154928000-154928800	Active TSS	Colonic Mucosa	Colon
49	chr1:154928000-154928800	Active TSS	GM12878-XiMat	blood
50	chr1:154928000-154929000	Active TSS	H1 Cell Line	embryonic stem cell

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