Variant report

Variant	rs2280995
Chromosome Location	chr1:166846069-166846070
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	KAP1	chr1:166845357-166846181	HEK293	kidney:	n/a	n/a
2	USF1	chr1:166845349-166846106	HCT-116	colon:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845689-166845698 chr1:166845683-166845704 chr1:166845688-166845697
3	MAX	chr1:166844830-166846076	NB4	blood:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
4	USF1	chr1:166845241-166846153	HCT-116	colon:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845689-166845698 chr1:166845683-166845704 chr1:166845688-166845697
5	RFX5	chr1:166844768-166846488	Hela-S3	cervix:	n/a	chr1:166845499-166845514
6	MAX	chr1:166844796-166846110	MCF-7	breast:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
7	BRCA1	chr1:166845299-166846120	Hela-S3	cervix:	n/a	n/a
8	USF1	chr1:166845345-166846070	K562	blood:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845689-166845698 chr1:166845683-166845704 chr1:166845688-166845697
9	SP1	chr1:166844580-166846121	HCT-116	colon:	n/a	chr1:166845323-166845332 chr1:166845581-166845595 chr1:166845581-166845590 chr1:166845580-166845592 chr1:166845582-166845591 chr1:166845580-166845592 chr1:166844993-166845002 chr1:166845580-166845591 chr1:166845737-166845746 chr1:166845622-166845634 chr1:166845674-166845686 chr1:166845736-166845748 chr1:166844991-166845003
10	WRNIP1	chr1:166845352-166846076	GM12878	blood:	n/a	n/a
11	CUX1	chr1:166845307-166846128	K562	blood:	n/a	n/a
12	POLR2A	chr1:166844561-166846174	PBDE	blood:	n/a	n/a
13	HCFC1	chr1:166843850-166846380	Hela-S3	cervix:	n/a	n/a
14	MAX	chr1:166844490-166846195	HCT-116	colon:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
15	PML	chr1:166844632-166846171	GM12878	blood:	n/a	n/a
16	MAX	chr1:166844490-166846141	A549	lung:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
17	CEBPB	chr1:166845605-166846105	A549	lung:	n/a	n/a
18	IRF1	chr1:166845279-166846131	K562	blood:	n/a	chr1:166845667-166845676 chr1:166845578-166845592
19	ZMIZ1	chr1:166845287-166846120	K562	blood:	n/a	n/a
20	MAZ	chr1:166844451-166846079	IMR90	lung:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
21	SP1	chr1:166844608-166846077	HCT-116	colon:	n/a	chr1:166845323-166845332 chr1:166845581-166845595 chr1:166845581-166845590 chr1:166845580-166845592 chr1:166845582-166845591 chr1:166845580-166845592 chr1:166844993-166845002 chr1:166845580-166845591 chr1:166845737-166845746 chr1:166845622-166845634 chr1:166845674-166845686 chr1:166845736-166845748 chr1:166844991-166845003
22	CBX3	chr1:166844471-166846096	HCT-116	colon:	n/a	n/a
23	SIN3AK20	chr1:166844714-166846137	MCF-7	breast:	n/a	n/a
24	TBL1XR1	chr1:166845372-166846129	K562	blood:	n/a	n/a
25	CEBPB	chr1:166845328-166846103	Hela-S3	cervix:	n/a	n/a
26	MAX	chr1:166844780-166846109	HCT-116	colon:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845687-166845700 chr1:166845684-166845703 chr1:166845688-166845699 chr1:166845690-166845699 chr1:166845689-166845698 chr1:166845687-166845700
27	MXI1	chr1:166844380-166846220	SK-N-SH	brain:	n/a	n/a
28	CBX3	chr1:166844475-166846122	K562	blood:	n/a	n/a
29	HA-E2F1	chr1:166844520-166846098	MCF-7	breast:	n/a	chr1:166845132-166845144 chr1:166845673-166845684 chr1:166845269-166845279 chr1:166845268-166845277
30	TBP	chr1:166845325-166846073	GM12878	blood:	n/a	n/a
31	BHLHE40	chr1:166844608-166846118	K562	blood:	n/a	chr1:166845689-166845698 chr1:166845687-166845700 chr1:166845689-166845698 chr1:166845683-166845704 chr1:166845688-166845697
32	CTCF	chr1:166845441-166846194	K562	blood:	n/a	n/a
33	ZKSCAN1	chr1:166844685-166846074	Hela-S3	cervix:	n/a	n/a

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr1:166846026-166846076	AG09309	skin:	n/a
2	chr1:166846026-166846076	K562	blood:	n/a
3	chr1:166846026-166846076	GM12892	blood:	n/a
4	chr1:166846026-166846076	GM12891	blood:	n/a
5	chr1:166846026-166846076	SK-N-SH	brain:	n/a
6	chr1:166846026-166846076	HRE	kidney:	n/a
7	chr1:166846026-166846076	SK-N-SH_RA	brain:	n/a
8	chr1:166846026-166846076	MCF10A-Er-Src	breast:	n/a
9	chr1:166846026-166846076	HCF	heart:	n/a
10	chr1:166846026-166846076	RPTEC	kidney:	n/a
11	chr1:166846026-166846076	BJ	skin:	n/a
12	chr1:166846026-166846076	GM19239	blood:	n/a
13	chr1:166846026-166846076	AG09319	gingival:	n/a
14	chr1:166846026-166846076	CMK	blood:	n/a
15	chr1:166846026-166846076	GM12878	blood:	n/a
16	chr1:166846026-166846076	HCPEpiC	choroid plexus:	n/a
17	chr1:166846026-166846076	ovcar-3	ovarian:	n/a
18	chr1:166846026-166846076	NB4	blood:	n/a
19	chr1:166846026-166846076	NHBE	bronchial:	n/a
20	chr1:166846026-166846076	SAEC	small airway:	n/a
21	chr1:166846026-166846076	PFSK-1	brain:	n/a
22	chr1:166846026-166846076	AoSMC	blood vessel:	n/a
23	chr1:166846026-166846076	HMEC	breast:	n/a
24	chr1:166846026-166846076	AG04449	skin:	fetal
25	chr1:166846026-166846076	HL-60	blood:	n/a
26	chr1:166846026-166846076	HRCEpiC	kidney:	n/a
27	chr1:166846026-166846076	HepG2	liver:	n/a
28	chr1:166846026-166846076	A549	lung:	n/a
29	chr1:166846026-166846076	NH-A	brain:	n/a
30	chr1:166846026-166846076	PANC-1	pancreas:	n/a
31	chr1:166846026-166846076	HRPEpiC	eye:	n/a
32	chr1:166846026-166846076	HIPEpiC	eye:	n/a
33	chr1:166846026-166846076	Hepatocyte	liver:	n/a
34	chr1:166846026-166846076	U87	brain:	n/a
35	chr1:166846026-166846076	HAEpiC	amniotic membrane:	n/a
36	chr1:166846026-166846076	LNCaP	prostate:	n/a
37	chr1:166846026-166846076	PrEC	prostate:	n/a
38	chr1:166846026-166846076	SK-N-MC	brain:	n/a
39	chr1:166846026-166846076	NT2-D1	testis:	n/a
40	chr1:166846026-166846076	HPAEpiC	pulmonary alveolar:	n/a
41	chr1:166846026-166846076	MCF-7	breast:	n/a
42	chr1:166846026-166846076	HEK293	kidney:	embryo
43	chr1:166846026-166846076	BE2_C	brain:	n/a
44	chr1:166846026-166846076	AG04450	lung:	fetal
45	chr1:166846026-166846076	HUVEC	blood vessel:	n/a
46	chr1:166846026-166846076	NHDF-neo	bronchial:	n/a
47	chr1:166846026-166846076	HCM	heart:	n/a
48	chr1:166846026-166846076	ECC-1	luminal epithelium:	n/a
49	chr1:166846026-166846076	HCT-116	colon:	n/a
50	chr1:166846026-166846076	AG10803	skin:	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:166458815..166461765-chr1:166845065..166847210,2	MCF-7	breast:
2	chr1:166805959..166811139-chr1:166841080..166848642,15	MCF-7	breast:
3	chr1:166832382..166838058-chr1:166843027..166847962,8	MCF-7	breast:
4	chr1:166806593..166810261-chr1:166844073..166846866,6	K562	blood:
5	chr1:166805232..166812474-chr1:166842359..166847542,11	MCF-7	breast:

Variant related genes	Relation type
TADA1	TF binding region
TADA1	CpG island
ENSG00000143157	Chromatin interaction
ENSG00000234142	Chromatin interaction
ENSG00000225171	Chromatin interaction
ENSG00000152382	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10800270	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10800276	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10918599	0.81[EUR][1000 genomes]
rs10918600	0.82[CEU][hapmap];0.95[TSI][hapmap];0.81[EUR][1000 genomes]
rs10918603	0.85[TSI][hapmap]
rs11576455	0.88[EUR][1000 genomes]
rs11579987	0.82[CEU][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap]
rs11583927	1.00[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11584352	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12062326	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12562794	0.94[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1476347	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1543313	0.97[ASN][1000 genomes]
rs2072740	0.97[ASN][1000 genomes]
rs2075946	0.94[CEU][hapmap];0.82[CHB][hapmap];0.82[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.81[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2142615	0.82[CEU][hapmap];0.81[EUR][1000 genomes]
rs2223221	0.98[ASN][1000 genomes]
rs2235184	0.88[CEU][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.88[EUR][1000 genomes]
rs2294195	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs34381372	1.00[ASN][1000 genomes]
rs3820387	0.94[CEU][hapmap];0.90[GIH][hapmap];0.81[JPT][hapmap];0.91[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4656516	1.00[ASN][1000 genomes]
rs4657609	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4657612	0.98[ASN][1000 genomes]
rs4657613	0.89[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];0.92[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6427047	0.88[CEU][hapmap];0.86[TSI][hapmap];0.80[EUR][1000 genomes]
rs742048	0.82[CEU][hapmap];0.95[TSI][hapmap]
rs7513457	0.98[ASN][1000 genomes]
rs7545806	0.85[TSI][hapmap]
rs9633326	1.00[CHB][hapmap];0.98[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916491	chr1:166000783-166948513	Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2280995	B4GALT3	cis	parietal	SCAN
rs2280995	RGS4	cis	parietal	SCAN

Chromatin state (count:95 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:166844000-166846200	Active TSS	HUES6 Cell Line	embryonic stem cell
2	chr1:166844200-166846200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr1:166844200-166846200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:166844400-166846200	Active TSS	ES-I3 Cell Line	embryonic stem cell
5	chr1:166844400-166846200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
6	chr1:166844400-166846200	Active TSS	iPS-15b Cell Line	embryonic stem cell
7	chr1:166844400-166846200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr1:166844400-166846200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr1:166844400-166846200	Active TSS	NHDF-Ad	bronchial
10	chr1:166844600-166846200	Active TSS	H1 Cell Line	embryonic stem cell
11	chr1:166844800-166846200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr1:166844800-166846200	Active TSS	iPS-18 Cell Line	embryonic stem cell
13	chr1:166844800-166846200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:166844800-166846200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr1:166844800-166846200	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr1:166844800-166846200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:166844800-166846200	Active TSS	Brain Cingulate Gyrus	brain
18	chr1:166844800-166846200	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
19	chr1:166844800-166846200	Active TSS	Brain Substantia Nigra	brain
20	chr1:166844800-166846200	Active TSS	Duodenum Smooth Muscle	Duodenum
21	chr1:166844800-166846200	Active TSS	Fetal Brain Female	brain
22	chr1:166844800-166846200	Active TSS	Rectal Mucosa Donor 31	rectum
23	chr1:166844800-166846200	Active TSS	Right Ventricle	heart
24	chr1:166844800-166846200	Active TSS	NHLF	lung
25	chr1:166845000-166846200	Active TSS	Breast Myoepithelial Primary Cells	Breast
26	chr1:166845000-166846200	Active TSS	Primary T cells fromperipheralblood	blood
27	chr1:166845000-166846200	Active TSS	Cortex derived primary cultured neurospheres	brain
28	chr1:166845000-166846200	Active TSS	Brain Angular Gyrus	brain
29	chr1:166845000-166846200	Active TSS	Fetal Intestine Small	intestine
30	chr1:166845000-166846200	Active TSS	Fetal Kidney	kidney
31	chr1:166845000-166846200	Active TSS	Fetal Muscle Trunk	muscle
32	chr1:166845000-166846200	Active TSS	Placenta	Placenta
33	chr1:166845000-166846200	Active TSS	Fetal Thymus	thymus
34	chr1:166845000-166846200	Active TSS	Skeletal Muscle Female	skeletal muscle
35	chr1:166845000-166846200	Active TSS	Stomach Smooth Muscle	stomach
36	chr1:166845000-166846200	Active TSS	NHEK	skin
37	chr1:166845000-166846400	Active TSS	K562	blood
38	chr1:166845400-166846200	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:166845400-166846200	Active TSS	Brain Germinal Matrix	brain
40	chr1:166845600-166846200	Active TSS	Right Atrium	heart
41	chr1:166845800-166846200	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr1:166845800-166846200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr1:166845800-166846200	Flanking Active TSS	Primary T cells from cord blood	blood
44	chr1:166845800-166846200	Flanking Active TSS	Primary hematopoietic stem cells	blood
45	chr1:166845800-166846200	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
46	chr1:166845800-166846200	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
47	chr1:166845800-166846200	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
48	chr1:166845800-166846200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
49	chr1:166845800-166846200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
50	chr1:166845800-166846200	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood

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