Variant report

Variant	rs1667601
Chromosome Location	chr2:74406055-74406056
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:428)
CpG islands
(count:122)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:428 , 50 per page) page: 1 2 3 4 5 6 7 ... 9

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPD	chr2:74405723-74406239	K562	blood:	n/a	n/a
2	MYC	chr2:74405287-74406284	NB4	blood:	n/a	chr2:74405684-74405694
3	POU2F2	chr2:74405174-74406327	GM12878	blood:	n/a	n/a
4	TAF1	chr2:74405254-74406278	Hela-S3	cervix:	n/a	n/a
5	BACH1	chr2:74406003-74406203	H1-hESC	embryonic stem cell:	n/a	n/a
6	YY1	chr2:74405860-74406367	ECC-1	luminal epithelium:	n/a	n/a
7	MAX	chr2:74405168-74406379	MCF-7	breast:	n/a	chr2:74405684-74405694
8	FOS	chr2:74406004-74406134	MCF10A-Er-Src	breast:	n/a	n/a
9	YY1	chr2:74405918-74406289	H1-hESC	embryonic stem cell:	n/a	n/a
10	ELF1	chr2:74405356-74406654	GM12878	blood:	n/a	chr2:74406133-74406142 chr2:74406041-74406053 chr2:74405478-74405490 chr2:74405685-74405697
11	CTCF	chr2:74406040-74406190	HEEpiC	esophagus:	n/a	n/a
12	NRF1	chr2:74405907-74406233	K562	blood:	n/a	n/a
13	ZNF143	chr2:74405336-74406358	GM12878	blood:	n/a	chr2:74406046-74406064 chr2:74406041-74406051 chr2:74406123-74406141
14	ZNF384	chr2:74405315-74406791	GM12878	blood:	n/a	n/a
15	TBP	chr2:74405815-74406346	HepG2	liver:	n/a	n/a
16	PAX5	chr2:74405167-74406696	GM12878	blood:	n/a	chr2:74405576-74405595 chr2:74406400-74406419 chr2:74406426-74406445
17	TBL1XR1	chr2:74405026-74406364	K562	blood:	n/a	n/a
18	POLR2A	chr2:74405147-74406472	SK-N-SH	brain:	n/a	n/a
19	UBTF	chr2:74405135-74406276	K562	blood:	n/a	n/a
20	POLR2A	chr2:74405808-74406075	H1-hESC	embryonic stem cell:	n/a	n/a
21	POLR2A	chr2:74405135-74406355	GM12892	blood:	n/a	n/a
22	SIN3AK20	chr2:74405031-74406883	MCF-7	breast:	n/a	n/a
23	POLR2A	chr2:74405530-74406530	MCF-7	breast:	n/a	n/a
24	PML	chr2:74405711-74406462	MCF-7	breast:	n/a	n/a
25	MXI1	chr2:74405956-74406324	K562	blood:	n/a	n/a
26	TAF1	chr2:74405228-74406324	GM12892	blood:	n/a	n/a
27	RUNX3	chr2:74405167-74406721	GM12878	blood:	n/a	n/a
28	POLR2A	chr2:74405767-74406143	HepG2	liver:	n/a	n/a
29	MXI1	chr2:74405268-74406286	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:74405352-74406304	Hela-S3	cervix:	n/a	n/a
31	POLR2A	chr2:74405599-74406429	U87	brain:	n/a	n/a
32	HEY1	chr2:74405367-74406346	HepG2	liver:	n/a	n/a
33	HA-E2F1	chr2:74405272-74406407	MCF-7	breast:	n/a	chr2:74405680-74405689 chr2:74406096-74406105 chr2:74405501-74405513
34	GTF2F1	chr2:74405849-74406261	K562	blood:	n/a	n/a
35	CHD2	chr2:74405308-74406350	HepG2	liver:	n/a	n/a
36	TAF7	chr2:74405474-74406324	H1-hESC	embryonic stem cell:	n/a	n/a
37	POLR2A	chr2:74405338-74406423	PBDE	blood:	n/a	n/a
38	POLR2A	chr2:74405002-74406377	GM12892	blood:	n/a	n/a
39	NFYA	chr2:74405979-74406286	K562	blood:	n/a	chr2:74406094-74406109 chr2:74406094-74406112 chr2:74406094-74406109 chr2:74406093-74406105
40	PML	chr2:74405091-74406691	GM12878	blood:	n/a	n/a
41	TAF1	chr2:74405721-74406434	MCF-7	breast:	n/a	n/a
42	ATF2	chr2:74405847-74406508	GM12878	blood:	n/a	n/a
43	YY1	chr2:74405825-74406246	HCT-116	colon:	n/a	n/a
44	POLR2A	chr2:74404833-74406456	GM12878	blood:	n/a	n/a
45	CTCF	chr2:74405960-74406110	HFF-Myc	foreskin:	n/a	n/a
46	RUNX3	chr2:74405134-74406705	GM12878	blood:	n/a	n/a
47	EP300	chr2:74405249-74406554	GM12878	blood:	n/a	n/a
48	HEY1	chr2:74405480-74406384	K562	blood:	n/a	n/a
49	ELF1	chr2:74405560-74406314	HepG2	liver:	n/a	chr2:74406133-74406142 chr2:74406041-74406053 chr2:74405685-74405697
50	SIN3AK20	chr2:74405189-74406268	PANC-1	pancreas:	n/a	n/a

(count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:74406045-74406095	AG04449	skin:	fetal
2	chr2:74406045-74406095	ProgFib	skin:	n/a
3	chr2:74406040-74406090	PrEC	prostate:	n/a
4	chr2:74406045-74406095	GM12878	blood:	n/a
5	chr2:74406045-74406095	HNPCEpiC	eye:	n/a
6	chr2:74406045-74406095	K562	blood:	n/a
7	chr2:74406040-74406090	ovcar-3	ovarian:	n/a
8	chr2:74406040-74406090	Jurkat	blood:	n/a
9	chr2:74406045-74406095	ECC-1	luminal epithelium:	n/a
10	chr2:74406040-74406090	K562	blood:	n/a
11	chr2:74406045-74406095	HCF	heart:	n/a
12	chr2:74406045-74406095	Hela-S3	cervix:	n/a
13	chr2:74406040-74406090	RPTEC	kidney:	n/a
14	chr2:74406040-74406090	SK-N-SH_RA	brain:	n/a
15	chr2:74406045-74406095	IMR90	lung:	fetal
16	chr2:74406045-74406095	GM12891	blood:	n/a
17	chr2:74406040-74406090	HUVEC	blood vessel:	n/a
18	chr2:74406040-74406090	HPAEpiC	pulmonary alveolar:	n/a
19	chr2:74406045-74406095	Jurkat	blood:	n/a
20	chr2:74406040-74406090	HEEpiC	esophagus:	n/a
21	chr2:74406040-74406090	Caco-2	colon:	n/a
22	chr2:74406040-74406090	IMR90	lung:	fetal
23	chr2:74406045-74406095	HAEpiC	amniotic membrane:	n/a
24	chr2:74406040-74406090	Hepatocyte	liver:	n/a
25	chr2:74406045-74406095	ovcar-3	ovarian:	n/a
26	chr2:74406045-74406095	HRPEpiC	eye:	n/a
27	chr2:74406040-74406090	SKMC	muscle:	n/a
28	chr2:74406045-74406095	PrEC	prostate:	n/a
29	chr2:74406040-74406090	NB4	blood:	n/a
30	chr2:74406045-74406095	HRE	kidney:	n/a
31	chr2:74406040-74406090	NHDF-neo	bronchial:	n/a
32	chr2:74406045-74406095	AG04450	lung:	fetal
33	chr2:74406040-74406090	HAEpiC	amniotic membrane:	n/a
34	chr2:74406045-74406095	NHDF-neo	bronchial:	n/a
35	chr2:74406040-74406090	HMEC	breast:	n/a
36	chr2:74406045-74406095	SKMC	muscle:	n/a
37	chr2:74406040-74406090	HRE	kidney:	n/a
38	chr2:74406045-74406095	AG09309	skin:	n/a
39	chr2:74406045-74406095	Hepatocyte	liver:	n/a
40	chr2:74406045-74406095	SK-N-SH_RA	brain:	n/a
41	chr2:74406040-74406090	HCPEpiC	choroid plexus:	n/a
42	chr2:74406040-74406090	SK-N-MC	brain:	n/a
43	chr2:74406045-74406095	AoSMC	blood vessel:	n/a
44	chr2:74406040-74406090	GM12878	blood:	n/a
45	chr2:74406045-74406095	NB4	blood:	n/a
46	chr2:74406040-74406090	AG04450	lung:	fetal
47	chr2:74406045-74406095	AG09319	gingival:	n/a
48	chr2:74406045-74406095	Caco-2	colon:	n/a
49	chr2:74406040-74406090	HCF	heart:	n/a
50	chr2:74406040-74406090	HNPCEpiC	eye:	n/a

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:74405644..74406366-chr5:1799519..1800033,2	Hela-S3	cervix:
2	chr2:74400907..74407799-chr2:74422654..74428562,23	MCF-7	breast:
3	chr2:74373512..74376720-chr2:74404630..74408955,6	K562	blood:
4	chr19:58919435..58920381-chr2:74405595..74406159,2	HCT-116	colon:
5	chr2:74372636..74376479-chr2:74402961..74407334,5	K562	blood:
6	chr2:74405127..74407896-chr2:74418355..74421991,4	MCF-7	breast:
7	chr2:74401100..74409624-chr2:74423713..74427389,30	MCF-7	breast:
8	chr2:74372816..74377340-chr2:74403923..74407839,6	MCF-7	breast:

No data

Variant related genes	Relation type
MOB1A	TF binding region
MOB1A	CpG island
ENSG00000171574	Chromatin interaction
ENSG00000171421	Chromatin interaction
ENSG00000065911	Chromatin interaction
ENSG00000267958	Chromatin interaction
ENSG00000232098	Chromatin interaction
ENSG00000225439	Chromatin interaction
ENSG00000163170	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11126426	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12196	0.84[CEU][hapmap]
rs13426653	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1620482	0.84[CEU][hapmap];0.84[CHB][hapmap];0.96[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1667605	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1667606	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1667609	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1723285	0.85[CEU][hapmap]
rs1723292	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3108164	0.88[CEU][hapmap]
rs34611905	0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35864597	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6546893	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6546894	0.87[ASN][1000 genomes]
rs702462	0.88[CEU][hapmap]
rs702466	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7340453	0.88[CEU][hapmap]
rs7559252	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7562297	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8001	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs828853	0.86[ASN][1000 genomes]
rs828856	0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs828858	0.88[CEU][hapmap]
rs828873	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828876	0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs828877	0.88[CEU][hapmap];0.84[CHB][hapmap];0.84[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs828882	0.92[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828883	0.92[CEU][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828884	0.92[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828885	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs828886	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828888	0.92[CEU][hapmap];0.86[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs828889	0.88[CEU][hapmap];0.87[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs828903	0.88[CEU][hapmap];0.89[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844168	0.96[CEU][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.91[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	nsv874286	chr2:74323500-74436721	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
2	esv3427010	chr2:74351730-74813541	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	140 gene(s)	inside rSNPs	diseases
3	nsv834261	chr2:74391709-74613720	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	81 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1667601	CYP26B1	cis	cerebellum	SCAN
rs1667601	MTHFD2	cis	lymphoblastoid	seeQTL

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:74402400-74406600	Active TSS	GM12878-XiMat	blood
2	chr2:74404000-74406600	Active TSS	HUES64 Cell Line	embryonic stem cell
3	chr2:74404000-74406600	Active TSS	Fetal Kidney	kidney
4	chr2:74404000-74406800	Active TSS	NHLF	lung
5	chr2:74404200-74406400	Active TSS	NH-A	brain
6	chr2:74404200-74406600	Active TSS	HSMM	muscle
7	chr2:74404200-74406800	Active TSS	iPS-20b Cell Line	embryonic stem cell
8	chr2:74404400-74406400	Active TSS	ES-I3 Cell Line	embryonic stem cell
9	chr2:74404400-74406400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr2:74404400-74406400	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr2:74404400-74406400	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr2:74404400-74406400	Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr2:74404400-74406400	Active TSS	K562	blood
14	chr2:74404400-74406600	Active TSS	HUES6 Cell Line	embryonic stem cell
15	chr2:74404400-74406600	Active TSS	iPS-18 Cell Line	embryonic stem cell
16	chr2:74404400-74406600	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr2:74404400-74406600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr2:74404400-74406600	Active TSS	Ovary	ovary
19	chr2:74404400-74406600	Active TSS	Right Atrium	heart
20	chr2:74404400-74406800	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr2:74404400-74406800	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
22	chr2:74404400-74406800	Active TSS	Brain Angular Gyrus	brain
23	chr2:74404400-74406800	Active TSS	Rectal Mucosa Donor 29	rectum
24	chr2:74404400-74406800	Active TSS	HMEC	breast
25	chr2:74404600-74406400	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr2:74404600-74406400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr2:74404600-74406400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr2:74404600-74406400	Active TSS	Primary T cells fromperipheralblood	blood
29	chr2:74404600-74406400	Active TSS	Primary hematopoietic stem cells short term culture	blood
30	chr2:74404600-74406400	Active TSS	Primary T helper naive cells from peripheral blood	blood
31	chr2:74404600-74406400	Active TSS	Primary Natural Killer cells fromperipheralblood	blood
32	chr2:74404600-74406400	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:74404600-74406400	Active TSS	Brain Inferior Temporal Lobe	brain
34	chr2:74404600-74406400	Active TSS	Fetal Brain Male	brain
35	chr2:74404600-74406400	Active TSS	Fetal Muscle Leg	muscle
36	chr2:74404600-74406400	Active TSS	Thymus	Thymus
37	chr2:74404600-74406400	Active TSS	NHEK	skin
38	chr2:74404600-74406600	Active TSS	H1 Cell Line	embryonic stem cell
39	chr2:74404600-74406600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:74404600-74406600	Active TSS	HUES48 Cell Line	embryonic stem cell
41	chr2:74404600-74406600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr2:74404600-74406600	Active TSS	Primary T killer memory cells from peripheral blood	blood
43	chr2:74404600-74406600	Active TSS	Muscle Satellite Cultured Cells	--
44	chr2:74404600-74406600	Active TSS	Brain Cingulate Gyrus	brain
45	chr2:74404600-74406600	Active TSS	Fetal Intestine Large	intestine
46	chr2:74404600-74406600	Active TSS	NHDF-Ad	bronchial
47	chr2:74404600-74406800	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
48	chr2:74404600-74406800	Active TSS	Colonic Mucosa	Colon
49	chr2:74404600-74406800	Active TSS	Duodenum Smooth Muscle	Duodenum
50	chr2:74404600-74406800	Active TSS	A549	lung

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