Variant report

Variant	rs59321380
Chromosome Location	chr3:47021780-47021781
allele	G/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	MAX	chr3:47021451-47021824	A549	lung:	n/a	n/a
2	MXI1	chr3:47020475-47021913	IMR90	lung:	n/a	n/a
3	RCOR1	chr3:47020556-47021805	K562	blood:	n/a	n/a
4	UBTF	chr3:47020623-47021834	K562	blood:	n/a	n/a
5	MAX	chr3:47020395-47021897	A549	lung:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
6	HA-E2F1	chr3:47020589-47021847	MCF-7	breast:	n/a	chr3:47020871-47020880 chr3:47020710-47020722 chr3:47020890-47020901 chr3:47021293-47021302 chr3:47021236-47021245
7	HCFC1	chr3:47020564-47021913	Hela-S3	cervix:	n/a	n/a
8	MAX	chr3:47020752-47021804	MCF-7	breast:	n/a	n/a
9	CTBP2	chr3:47020488-47021916	H1-hESC	embryonic stem cell:	n/a	n/a
10	E2F6	chr3:47020405-47021786	H1-hESC	embryonic stem cell:	n/a	chr3:47020871-47020880 chr3:47020710-47020722 chr3:47020890-47020901 chr3:47021316-47021328 chr3:47021293-47021302 chr3:47021236-47021245
11	MAZ	chr3:47020868-47021995	GM12878	blood:	n/a	n/a
12	YY1	chr3:47020571-47021859	HepG2	liver:	n/a	chr3:47020665-47020676 chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
13	MXI1	chr3:47020382-47022110	SK-N-SH	brain:	n/a	n/a
14	MAX	chr3:47020321-47021924	K562	blood:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
15	POLR2A	chr3:47020633-47021912	HUVEC	blood vessel:	n/a	n/a
16	SIN3A	chr3:47020624-47021920	H1-hESC	embryonic stem cell:	n/a	chr3:47021236-47021247
17	POLR2A	chr3:47020331-47021965	Raji	blood:	n/a	n/a
18	POLR2A	chr3:47021713-47022639	MCF-7	breast:	n/a	n/a
19	HEY1	chr3:47021451-47021805	K562	blood:	n/a	n/a
20	EGR1	chr3:47021487-47021781	K562	blood:	n/a	chr3:47021634-47021648 chr3:47021638-47021647 chr3:47021637-47021650
21	MYC	chr3:47020777-47021850	A549	lung:	n/a	n/a
22	POLR2A	chr3:47020484-47021835	GM12892	blood:	n/a	n/a
23	MAX	chr3:47020556-47021840	ECC-1	luminal epithelium:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
24	BHLHE40	chr3:47020892-47021819	GM12878	blood:	n/a	n/a
25	POLR2A	chr3:47020562-47021866	HL-60	blood:	n/a	n/a
26	YY1	chr3:47020484-47021802	K562	blood:	n/a	chr3:47020665-47020676 chr3:47021013-47021024 chr3:47020871-47020880 chr3:47021143-47021152 chr3:47021109-47021123 chr3:47021107-47021118 chr3:47021293-47021302
27	GTF3C2	chr3:47020569-47021945	K562	blood:	n/a	n/a
28	MAX	chr3:47020471-47021783	Hela-S3	cervix:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
29	POLR2A	chr3:47021765-47021946	MCF-7	breast:	n/a	n/a
30	MAX	chr3:47020425-47021846	HepG2	liver:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
31	EGR1	chr3:47021472-47021787	K562	blood:	n/a	chr3:47021634-47021648 chr3:47021638-47021647 chr3:47021637-47021650
32	MAX	chr3:47020405-47021800	HepG2	liver:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
33	ZBTB7A	chr3:47021699-47022086	K562	blood:	n/a	chr3:47021835-47021846 chr3:47021834-47021845
34	MAX	chr3:47020872-47021904	NB4	blood:	n/a	n/a
35	STAT5A	chr3:47021547-47021822	GM12878	blood:	n/a	n/a
36	POLR2A	chr3:47020469-47022022	K562	blood:	n/a	n/a
37	ELF1	chr3:47020462-47021871	GM12878	blood:	n/a	chr3:47021334-47021346 chr3:47021698-47021710
38	POLR2A	chr3:47020485-47021816	Hela-S3	cervix:	n/a	n/a
39	MYC	chr3:47020716-47021953	NB4	blood:	n/a	n/a
40	MXI1	chr3:47020936-47021815	Hela-S3	cervix:	n/a	n/a
41	WRNIP1	chr3:47021770-47022416	GM12878	blood:	n/a	n/a
42	MAX	chr3:47020552-47021869	H1-hESC	embryonic stem cell:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
43	POLR2A	chr3:47020482-47021837	GM12878	blood:	n/a	n/a
44	MYC	chr3:47020489-47021844	K562	blood:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
45	MAX	chr3:47020594-47021908	ECC-1	luminal epithelium:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
46	MAZ	chr3:47020522-47021800	IMR90	lung:	n/a	chr3:47020613-47020623 chr3:47020626-47020635
47	JUN	chr3:47020315-47021981	K562	blood:	n/a	chr3:47021289-47021298 chr3:47021105-47021114
48	POLR2A	chr3:47020705-47021841	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:75185461..75186274-chr3:47021175..47021935,2	Hela-S3	cervix:
2	chr3:47020574..47023054-chr3:47051075..47053218,2	MCF-7	breast:
3	chr3:47019689..47022693-chr3:47040941..47043835,3	MCF-7	breast:
4	chr3:47019697..47022640-chr3:47324324..47326151,2	K562	blood:

Variant related genes	Relation type
CCDC12	TF binding region
ENSG00000160796	Chromatin interaction
ENSG00000088727	Chromatin interaction
ENSG00000115350	Chromatin interaction
ENSG00000114648	Chromatin interaction
ENSG00000236409	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10510753	0.81[AMR][1000 genomes]
rs17079331	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs17079336	0.83[AFR][1000 genomes]
rs2385870	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs4515087	0.81[AMR][1000 genomes]
rs57246717	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs57313197	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs58840220	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59295935	0.89[AFR][1000 genomes]
rs6442051	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs72905877	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72905900	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72907932	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs72907946	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7612808	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7632511	0.84[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv536558	chr3:46706571-47024756	Enhancers Bivalent Enhancer Active TSS Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	nsv876755	chr3:46895109-47061183	Genic enhancers Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
3	esv3461834	chr3:46977730-47173228	Active TSS Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	esv3461835	chr3:46977822-47173168	Enhancers Genic enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats 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	28 gene(s)	inside rSNPs	diseases
5	esv3461836	chr3:46977822-47173168	Weak transcription Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv1009396	chr3:46994991-47048166	Weak transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
7	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases
8	esv1800172	chr3:47013346-47049306	Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
9	nsv590209	chr3:47018214-47050784	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	18 gene(s)	inside rSNPs	diseases
10	nsv876757	chr3:47018214-47058057	Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	21 gene(s)	inside rSNPs	diseases
11	esv3359860	chr3:47019973-47022521	Active TSS Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	8 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	chr3:47020200-47021800	Active TSS	iPS-18 Cell Line	embryonic stem cell
2	chr3:47020400-47021800	Active TSS	ES-I3 Cell Line	embryonic stem cell
3	chr3:47020400-47021800	Active TSS	H9 Cell Line	embryonic stem cell
4	chr3:47020400-47021800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr3:47020400-47021800	Active TSS	Esophagus	oesophagus
6	chr3:47020400-47021800	Active TSS	Pancreas	Pancrea
7	chr3:47020400-47021800	Active TSS	Psoas Muscle	Psoas
8	chr3:47020400-47022000	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr3:47020400-47022000	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
10	chr3:47020400-47022000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr3:47020400-47022200	Active TSS	HUES48 Cell Line	embryonic stem cell
12	chr3:47020400-47022200	Active TSS	HUES6 Cell Line	embryonic stem cell
13	chr3:47020400-47022400	Active TSS	Fetal Kidney	kidney
14	chr3:47020400-47022600	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr3:47020400-47022600	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr3:47020600-47021800	Active TSS	Lung	lung
17	chr3:47020600-47021800	Active TSS	Small Intestine	intestine
18	chr3:47020600-47021800	Active TSS	HSMMtube	muscle
19	chr3:47020600-47022000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
20	chr3:47020600-47022000	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr3:47020600-47022000	Active TSS	Primary T killer memory cells from peripheral blood	blood
22	chr3:47020600-47022000	Active TSS	Aorta	Aorta
23	chr3:47020600-47022000	Active TSS	Colon Smooth Muscle	Colon
24	chr3:47020600-47022000	Active TSS	HSMM	muscle
25	chr3:47020600-47022200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr3:47020600-47022200	Active TSS	Left Ventricle	heart
27	chr3:47020600-47022200	Active TSS	Right Atrium	heart
28	chr3:47020600-47022400	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:47020600-47022600	Flanking Active TSS	HMEC	breast
30	chr3:47020600-47023800	Active TSS	Rectal Smooth Muscle	rectum
31	chr3:47020800-47021800	Active TSS	Breast Myoepithelial Primary Cells	Breast
32	chr3:47020800-47021800	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
33	chr3:47020800-47021800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr3:47020800-47021800	Active TSS	Ovary	ovary
35	chr3:47020800-47021800	Active TSS	Placenta Amnion	Placenta Amnion
36	chr3:47020800-47022000	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr3:47020800-47022000	Active TSS	Primary T helper naive cells from peripheral blood	blood
38	chr3:47020800-47022000	Active TSS	Duodenum Smooth Muscle	Duodenum
39	chr3:47020800-47022000	Active TSS	Hela-S3	cervix
40	chr3:47020800-47022200	Active TSS	Brain Anterior Caudate	brain
41	chr3:47020800-47022200	Active TSS	Stomach Mucosa	stomach
42	chr3:47020800-47022400	Active TSS	Brain Substantia Nigra	brain
43	chr3:47020800-47022400	Active TSS	A549	lung
44	chr3:47021000-47021800	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:47021000-47021800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr3:47021000-47021800	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
47	chr3:47021000-47021800	Active TSS	Colonic Mucosa	Colon
48	chr3:47021000-47021800	Active TSS	Spleen	Spleen
49	chr3:47021000-47021800	Active TSS	Monocytes-CD14+_RO01746	blood
50	chr3:47021000-47022000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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