Variant report

Variant	rs3731665
Chromosome Location	chr2:20189298-20189299
allele	C/T
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	chr2:20188774-20190793	H1-hESC	embryonic stem cell:	n/a	n/a
2	MAX	chr2:20188716-20190757	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
3	POLR2A	chr2:20189175-20190243	Hela-S3	cervix:	n/a	n/a
4	MAX	chr2:20189154-20190384	ECC-1	luminal epithelium:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
5	GTF2F1	chr2:20188987-20190060	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr2:20189218-20190194	SK-N-MC	brain:	n/a	n/a
7	MAX	chr2:20189210-20190453	HepG2	liver:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
8	MAX	chr2:20189006-20190598	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
9	ELK4	chr2:20189243-20190122	Hela-S3	cervix:	n/a	chr2:20189926-20189934 chr2:20189923-20189934 chr2:20189925-20189934
10	USF1	chr2:20189236-20189656	A549	lung:	n/a	chr2:20189435-20189446
11	MAX	chr2:20189292-20190366	HepG2	liver:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
12	MAX	chr2:20189258-20190206	A549	lung:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
13	MYC	chr2:20188852-20190373	MCF10A-Er-Src	breast:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
14	SIN3AK20	chr2:20189182-20190359	A549	lung:	n/a	n/a
15	TCF12	chr2:20188950-20190739	A549	lung:	n/a	n/a
16	MXI1	chr2:20189245-20190249	HepG2	liver:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
17	MAX	chr2:20189173-20190474	HCT-116	colon:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
18	USF1	chr2:20189214-20190183	A549	lung:	n/a	chr2:20189435-20189446
19	MXI1	chr2:20188819-20190128	Hela-S3	cervix:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
20	MAX	chr2:20189168-20190432	ECC-1	luminal epithelium:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
21	MAX	chr2:20189139-20190366	MCF-7	breast:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
22	E2F6	chr2:20189212-20190572	A549	lung:	n/a	chr2:20189964-20189973
23	MAX	chr2:20189172-20190450	HCT-116	colon:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
24	MXI1	chr2:20189292-20190357	H1-hESC	embryonic stem cell:	n/a	chr2:20189876-20189891 chr2:20189874-20189889
25	MAX	chr2:20189136-20190277	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
26	FOSL2	chr2:20189260-20190530	A549	lung:	n/a	n/a
27	MAX	chr2:20188829-20190479	SK-N-SH	brain:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
28	CEBPB	chr2:20189240-20189951	Hela-S3	cervix:	n/a	chr2:20189399-20189410
29	MAFK	chr2:20188984-20190023	Hela-S3	cervix:	n/a	n/a
30	POLR2A	chr2:20189199-20190228	MCF10A-Er-Src	breast:	n/a	n/a
31	YY1	chr2:20189294-20190231	H1-hESC	embryonic stem cell:	n/a	chr2:20189797-20189808
32	MAX	chr2:20189295-20190179	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
33	MAX	chr2:20189287-20190152	HUVEC	blood vessel:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
34	REST	chr2:20189243-20190510	A549	lung:	n/a	n/a
35	SIN3AK20	chr2:20189202-20190418	MCF-7	breast:	n/a	n/a
36	MYC	chr2:20188718-20190445	MCF10A-Er-Src	breast:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
37	POLR2A	chr2:20189225-20190537	SK-N-SH	brain:	n/a	n/a
38	USF2	chr2:20189264-20189641	Hela-S3	cervix:	n/a	n/a
39	MAX	chr2:20188915-20190245	H1-hESC	embryonic stem cell:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
40	IRF1	chr2:20189241-20189354	K562	blood:	n/a	n/a
41	TBP	chr2:20189251-20189917	Hela-S3	cervix:	n/a	n/a
42	CTBP2	chr2:20189259-20190275	H1-hESC	embryonic stem cell:	n/a	n/a
43	GABPA	chr2:20189150-20190306	A549	lung:	n/a	chr2:20189965-20189974 chr2:20189960-20189974 chr2:20189963-20189977 chr2:20189963-20189974
44	CEBPB	chr2:20189257-20189543	K562	blood:	n/a	chr2:20189399-20189410
45	MYC	chr2:20188953-20190035	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
46	SIN3AK20	chr2:20189001-20190283	SK-N-SH	brain:	n/a	n/a
47	GABPA	chr2:20189124-20190531	A549	lung:	n/a	chr2:20189965-20189974 chr2:20189960-20189974 chr2:20189963-20189977 chr2:20189963-20189974 chr2:20190433-20190440
48	MYC	chr2:20189220-20189568	K562	blood:	n/a	chr2:20189435-20189443 chr2:20189478-20189488 chr2:20189477-20189488 chr2:20189477-20189487 chr2:20189479-20189486 chr2:20189478-20189487 chr2:20189477-20189488 chr2:20189476-20189486 chr2:20189435-20189445 chr2:20189478-20189487
49	GABPA	chr2:20189068-20190646	MCF-7	breast:	n/a	chr2:20189965-20189974 chr2:20189960-20189974 chr2:20189963-20189977 chr2:20189963-20189974 chr2:20190433-20190440
50	E2F6	chr2:20189082-20190398	H1-hESC	embryonic stem cell:	n/a	chr2:20189964-20189973

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr2:20189267-20189317	NT2-D1	testis:	n/a
2	chr2:20189267-20189317	NHBE	bronchial:	n/a
3	chr2:20189267-20189317	Caco-2	colon:	n/a
4	chr2:20189267-20189317	HL-60	blood:	n/a
5	chr2:20189267-20189317	Jurkat	blood:	n/a
6	chr2:20189267-20189317	GM12878	blood:	n/a
7	chr2:20189267-20189317	NHDF-neo	bronchial:	n/a
8	chr2:20189267-20189317	H1-hESC	embryonic stem cell:	embryo
9	chr2:20189267-20189317	SK-N-SH	brain:	n/a
10	chr2:20189267-20189317	AoSMC	blood vessel:	n/a
11	chr2:20189267-20189317	HRE	kidney:	n/a
12	chr2:20189267-20189317	HNPCEpiC	eye:	n/a
13	chr2:20189267-20189317	HepG2	liver:	n/a
14	chr2:20189267-20189317	GM12891	blood:	n/a
15	chr2:20189267-20189317	GM12892	blood:	n/a
16	chr2:20189267-20189317	GM19239	blood:	n/a
17	chr2:20189267-20189317	SK-N-SH_RA	brain:	n/a
18	chr2:20189267-20189317	K562	blood:	n/a
19	chr2:20189267-20189317	A549	lung:	n/a
20	chr2:20189267-20189317	HCT-116	colon:	n/a
21	chr2:20189267-20189317	ovcar-3	ovarian:	n/a
22	chr2:20189267-20189317	T-47D	breast:	n/a
23	chr2:20189267-20189317	SKMC	muscle:	n/a
24	chr2:20189267-20189317	HRCEpiC	kidney:	n/a
25	chr2:20189267-20189317	PFSK-1	brain:	n/a
26	chr2:20189267-20189317	LNCaP	prostate:	n/a
27	chr2:20189267-20189317	NH-A	brain:	n/a
28	chr2:20189267-20189317	AG04450	lung:	fetal
29	chr2:20189267-20189317	PrEC	prostate:	n/a
30	chr2:20189267-20189317	NB4	blood:	n/a
31	chr2:20189267-20189317	HPAEpiC	pulmonary alveolar:	n/a
32	chr2:20189267-20189317	HUVEC	blood vessel:	n/a
33	chr2:20189267-20189317	SAEC	small airway:	n/a
34	chr2:20189267-20189317	RPTEC	kidney:	n/a
35	chr2:20189267-20189317	ECC-1	luminal epithelium:	n/a
36	chr2:20189267-20189317	HAEpiC	amniotic membrane:	n/a
37	chr2:20189267-20189317	IMR90	lung:	fetal
38	chr2:20189267-20189317	HIPEpiC	eye:	n/a
39	chr2:20189267-20189317	AG10803	skin:	n/a
40	chr2:20189267-20189317	SK-N-MC	brain:	n/a
41	chr2:20189267-20189317	PANC-1	pancreas:	n/a
42	chr2:20189267-20189317	Hela-S3	cervix:	n/a
43	chr2:20189267-20189317	HCPEpiC	choroid plexus:	n/a
44	chr2:20189267-20189317	U87	brain:	n/a
45	chr2:20189267-20189317	BJ	skin:	n/a
46	chr2:20189267-20189317	HEEpiC	esophagus:	n/a
47	chr2:20189267-20189317	HMEC	breast:	n/a
48	chr2:20189267-20189317	HRPEpiC	eye:	n/a
49	chr2:20189267-20189317	Hepatocyte	liver:	n/a
50	chr2:20189267-20189317	GM06990	blood:	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:20100581..20103342-chr2:20187181..20189808,2	K562	blood:
2	chr2:20187710..20189541-chr2:20212607..20214933,2	K562	blood:
3	chr2:20187189..20189541-chr2:20212582..20214933,2	K562	blood:
4	chr2:20100581..20103350-chr2:20187181..20189808,3	K562	blood:
5	chr2:20188544..20190994-chr2:20211302..20213941,2	MCF-7	breast:
6	chr2:20187273..20189318-chr2:20295101..20297253,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000227210	TF binding region
ENSG00000227210	CpG island
ENSG00000271991	Chromatin interaction
ENSG00000183891	Chromatin interaction
ENSG00000132031	Chromatin interaction

Extended variants
information (count: 14 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1030900	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12611974	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12614643	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12622939	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16987211	0.85[EUR][1000 genomes]
rs16987218	0.81[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs16987282	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2293670	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3731664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3795965	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55919320	1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];1.00[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	nsv1006404	chr2:20167688-20216509	Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv1005431	chr2:20174676-20210163	Enhancers Flanking Active TSS Genic enhancers Weak transcription Strong transcription Bivalent/Poised TSS Active 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 miRNA target site	7 gene(s)	inside rSNPs	diseases
3	nsv1011244	chr2:20174676-20216204	Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:20174200-20189400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr2:20185200-20189400	Weak transcription	Lung	lung
3	chr2:20188000-20190400	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr2:20188200-20190600	Active TSS	H9 Cell Line	embryonic stem cell
5	chr2:20188400-20189600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:20188400-20190600	Active TSS	Brain Cingulate Gyrus	brain
7	chr2:20188600-20189400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:20188600-20189600	Flanking Active TSS	Osteobl	bone
9	chr2:20188600-20190000	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr2:20188600-20190000	Active TSS	NHLF	lung
11	chr2:20188600-20190200	Active TSS	K562	blood
12	chr2:20188600-20190600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr2:20188600-20190800	Active TSS	H1 Cell Line	embryonic stem cell
14	chr2:20188800-20189400	Enhancers	Primary monocytes fromperipheralblood	blood
15	chr2:20188800-20189400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
16	chr2:20188800-20189400	Flanking Active TSS	Brain Germinal Matrix	brain
17	chr2:20188800-20189400	Flanking Active TSS	Fetal Brain Female	brain
18	chr2:20188800-20189400	Flanking Active TSS	NHEK	skin
19	chr2:20188800-20189600	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr2:20188800-20189600	Flanking Active TSS	Brain Angular Gyrus	brain
21	chr2:20188800-20189600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr2:20188800-20189600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
23	chr2:20188800-20189800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:20188800-20189800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr2:20188800-20190000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr2:20188800-20190000	Active TSS	Ovary	ovary
27	chr2:20188800-20190200	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr2:20188800-20190200	Active TSS	Fetal Stomach	stomach
29	chr2:20188800-20190400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
30	chr2:20188800-20190400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr2:20188800-20190400	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr2:20188800-20190400	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr2:20188800-20190400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
34	chr2:20188800-20190400	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr2:20188800-20190400	Flanking Active TSS	HUVEC	blood vessel
36	chr2:20188800-20190400	Active TSS	NHDF-Ad	bronchial
37	chr2:20188800-20190600	Active TSS	ES-I3 Cell Line	embryonic stem cell
38	chr2:20188800-20190600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
39	chr2:20188800-20190600	Active TSS	HUES48 Cell Line	embryonic stem cell
40	chr2:20188800-20190600	Active TSS	HUES64 Cell Line	embryonic stem cell
41	chr2:20188800-20190600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
42	chr2:20188800-20190600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
43	chr2:20188800-20190600	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr2:20188800-20190600	Active TSS	Psoas Muscle	Psoas
45	chr2:20188800-20190600	Active TSS	Right Atrium	heart
46	chr2:20188800-20190600	Active TSS	Right Ventricle	heart
47	chr2:20188800-20190600	Active TSS	HSMMtube	muscle
48	chr2:20188800-20190800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr2:20188800-20190800	Active TSS	Rectal Mucosa Donor 29	rectum
50	chr2:20189000-20189400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood

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