Variant report

Variant	rs9535420
Chromosome Location	chr13:50700048-50700049
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	PML	chr13:50699438-50700185	MCF-7	breast:	n/a	n/a
2	HA-E2F1	chr13:50699402-50700489	Hela-S3	cervix:	n/a	chr13:50699962-50699972 chr13:50700333-50700345 chr13:50699938-50699947 chr13:50699965-50699975 chr13:50699968-50699978 chr13:50700254-50700266
3	TCF7L2	chr13:50699933-50700544	PANC-1	pancreas:	n/a	n/a
4	USF1	chr13:50699716-50700064	A549	lung:	n/a	chr13:50699898-50699911 chr13:50699898-50699909 chr13:50699961-50699977 chr13:50699964-50699980 chr13:50699997-50700013 chr13:50699899-50699908 chr13:50699972-50699988 chr13:50699901-50699910 chr13:50699900-50699909 chr13:50699900-50699909
5	POLR2A	chr13:50699269-50700678	K562	blood:	n/a	n/a
6	MAX	chr13:50699594-50700400	SK-N-SH	brain:	n/a	chr13:50699900-50699909
7	UBTF	chr13:50697882-50700555	K562	blood:	n/a	n/a
8	BACH1	chr13:50699860-50700283	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr13:50697492-50700918	HL-60	blood:	n/a	n/a
10	NFIC	chr13:50699595-50700198	ECC-1	luminal epithelium:	n/a	n/a
11	MAZ	chr13:50697808-50700565	K562	blood:	n/a	chr13:50699900-50699909 chr13:50698347-50698357 chr13:50698675-50698684
12	RCOR1	chr13:50699773-50700687	HepG2	liver:	n/a	n/a
13	TBP	chr13:50699150-50700678	HepG2	liver:	n/a	n/a
14	YY1	chr13:50699669-50700463	H1-hESC	embryonic stem cell:	n/a	chr13:50699971-50699982 chr13:50700210-50700224 chr13:50699938-50699947 chr13:50699961-50699975 chr13:50699964-50699973 chr13:50699967-50699981 chr13:50699961-50699970 chr13:50699962-50699973 chr13:50699964-50699978
15	REST	chr13:50697831-50700776	HL-60	blood:	n/a	chr13:50698383-50698396 chr13:50699923-50699933 chr13:50698256-50698263 chr13:50698565-50698578 chr13:50698982-50698989 chr13:50700377-50700390
16	MAX	chr13:50699746-50700109	H1-hESC	embryonic stem cell:	n/a	chr13:50699900-50699909
17	POLR2A	chr13:50697801-50703833	H1-neurons	neurons:	n/a	n/a
18	TAF1	chr13:50699654-50700083	H1-neurons	neurons:	n/a	n/a
19	POLR2A	chr13:50697958-50700548	MCF-7	breast:	n/a	n/a
20	SMC3	chr13:50699733-50700869	Hela-S3	cervix:	n/a	n/a
21	BRCA1	chr13:50699662-50700053	Hela-S3	cervix:	n/a	n/a
22	EP300	chr13:50697831-50700604	ECC-1	luminal epithelium:	n/a	chr13:50699941-50699950 chr13:50699071-50699087 chr13:50699938-50699954 chr13:50698401-50698410 chr13:50699865-50699881 chr13:50699923-50699939 chr13:50699966-50699975 chr13:50699358-50699372 chr13:50699963-50699972
23	MAX	chr13:50699685-50700494	K562	blood:	n/a	chr13:50699900-50699909
24	UBTF	chr13:50697747-50700655	K562	blood:	n/a	n/a
25	POLR2A	chr13:50697750-50700484	MCF-7	breast:	n/a	n/a
26	JUN	chr13:50697272-50701175	K562	blood:	n/a	chr13:50698631-50698640 chr13:50699942-50699951 chr13:50698913-50698922 chr13:50698065-50698073 chr13:50698064-50698074 chr13:50698306-50698315 chr13:50698630-50698643 chr13:50698064-50698074 chr13:50698374-50698383 chr13:50698064-50698074 chr13:50700140-50700149
27	POLR2A	chr13:50699758-50700416	A549	lung:	n/a	n/a
28	POLR2A	chr13:50699389-50700379	HUVEC	blood vessel:	n/a	n/a
29	REST	chr13:50697619-50700820	H1-neurons	neurons:	n/a	chr13:50698383-50698396 chr13:50699923-50699933 chr13:50698256-50698263 chr13:50698565-50698578 chr13:50698982-50698989 chr13:50700377-50700390
30	POLR2A	chr13:50699615-50700171	HUVEC	blood vessel:	n/a	n/a
31	MAX	chr13:50699645-50700505	MCF-7	breast:	n/a	chr13:50699900-50699909
32	POLR2A	chr13:50699751-50700433	A549	lung:	n/a	n/a
33	USF2	chr13:50699741-50700091	HepG2	liver:	n/a	chr13:50699898-50699911 chr13:50699961-50699977 chr13:50699964-50699980 chr13:50699997-50700013 chr13:50699899-50699908 chr13:50699899-50699910 chr13:50699972-50699988 chr13:50699901-50699910 chr13:50699900-50699909 chr13:50699900-50699909
34	TCF7L2	chr13:50699806-50700774	Hela-S3	cervix:	n/a	n/a
35	YY1	chr13:50699587-50700476	HepG2	liver:	n/a	chr13:50699971-50699982 chr13:50700210-50700224 chr13:50699938-50699947 chr13:50699961-50699975 chr13:50699964-50699973 chr13:50699967-50699981 chr13:50699961-50699970 chr13:50699962-50699973 chr13:50699964-50699978
36	MYC	chr13:50697689-50701139	NB4	blood:	n/a	chr13:50699900-50699909 chr13:50698347-50698357 chr13:50698675-50698684
37	E2F6	chr13:50699710-50702123	H1-hESC	embryonic stem cell:	n/a	chr13:50699962-50699972 chr13:50701570-50701580 chr13:50700333-50700345 chr13:50701568-50701579 chr13:50699938-50699947 chr13:50699965-50699975 chr13:50700926-50700938 chr13:50699968-50699978 chr13:50701569-50701580 chr13:50700254-50700266 chr13:50700334-50700345
38	RUNX3	chr13:50699973-50700484	GM12878	blood:	n/a	n/a
39	CTCF	chr13:50699940-50700090	SAEC	small airway:	n/a	n/a
40	POLR2A	chr13:50699491-50700385	HepG2	liver:	n/a	n/a
41	MAX	chr13:50697935-50700814	HepG2	liver:	n/a	chr13:50699900-50699909 chr13:50698347-50698357 chr13:50698675-50698684
42	TAF1	chr13:50697918-50700554	ECC-1	luminal epithelium:	n/a	n/a
43	TCF3	chr13:50699766-50700055	GM12878	blood:	n/a	n/a
44	POLR2A	chr13:50699554-50700077	SK-N-SH	brain:	n/a	n/a
45	MAX	chr13:50699558-50700704	HCT-116	colon:	n/a	chr13:50699900-50699909
46	ELF1	chr13:50699848-50700291	K562	blood:	n/a	chr13:50699961-50699970 chr13:50699970-50699979 chr13:50699964-50699973 chr13:50699929-50699941 chr13:50699962-50699974 chr13:50699965-50699977 chr13:50700104-50700117
47	MYC	chr13:50700048-50700052	K562	blood:	n/a	n/a
48	RCOR1	chr13:50699682-50700680	Hela-S3	cervix:	n/a	n/a
49	MYC	chr13:50699648-50700451	MCF-7	breast:	n/a	chr13:50699900-50699909
50	ELF1	chr13:50699825-50700310	HepG2	liver:	n/a	chr13:50699961-50699970 chr13:50699970-50699979 chr13:50699964-50699973 chr13:50699929-50699941 chr13:50699962-50699974 chr13:50699965-50699977 chr13:50700104-50700117

No.	Distal block	Cell Line	Cell type
1	chr13:50696984..50702154-chr13:51483455..51488031,9	K562	blood:
2	chr13:50652169..50667024-chr13:50693268..50703943,57	K562	blood:
3	chr13:50696202..50700492-chr13:50759152..50762847,4	K562	blood:
4	chr13:50568991..50573569-chr13:50697831..50701767,8	K562	blood:
5	chr11:10829786..10830520-chr13:50699784..50700337,2	NB4	blood:
6	chr13:50699189..50701054-chr16:1428158..1429695,2	MCF-7	breast:
7	chr13:50699919..50702491-chr17:57916602..57918837,2	MCF-7	breast:
8	chr13:50569500..50573569-chr13:50696112..50701767,10	K562	blood:
9	chr13:50700031..50700747-chr19:10305314..10305988,2	Hela-S3	cervix:
10	chr13:50698611..50701082-chr13:51100302..51101813,2	MCF-7	breast:
11	chr13:50699687..50700540-chr19:10305003..10305663,2	NB4	blood:
12	chr13:50698913..50701877-chr17:56707826..56709440,2	MCF-7	breast:
13	chr13:50698526..50701372-chr13:50933812..50935948,3	MCF-7	breast:
14	chr13:50698015..50701526-chr13:51100615..51103673,4	MCF-7	breast:
15	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
16	chr13:50699219..50700050-chr3:12705651..12706196,2	NB4	blood:
17	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:
18	chr13:50699779..50700574-chr7:32930690..32931221,2	Hela-S3	cervix:
19	chr13:50696939..50701257-chr13:51483386..51488031,9	K562	blood:
20	chr13:50699976..50701803-chr13:51102949..51104727,2	MCF-7	breast:
21	chr13:50699752..50700375-chr2:70313380..70314095,2	NB4	blood:
22	chr13:50569368..50571479-chr13:50698927..50701104,2	MCF-7	breast:
23	chr13:50699509..50700060-chr2:61764889..61765534,2	NB4	blood:
24	chr13:50699751..50700379-chr2:203239793..203240452,2	MCF-7	breast:
25	chr13:50672721..50675302-chr13:50698038..50700346,2	K562	blood:
26	chr13:50653006..50665770-chr13:50696335..50703879,43	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KCNRG-2	chr13:50699952-50702599	NONHSAT033826

Variant related genes	Relation type
DLEU2	TF binding region
ENSG00000212195	Chromatin interaction
ENSG00000223676	Chromatin interaction
ENSG00000170852	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000273456	Chromatin interaction
ENSG00000082898	Chromatin interaction
ENSG00000229323	Chromatin interaction
ENSG00000130816	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000265529	Chromatin interaction
ENSG00000132155	Chromatin interaction
ENSG00000214359	Chromatin interaction
ENSG00000110321	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000059145	Chromatin interaction
ENSG00000179818	Chromatin interaction
ENSG00000233672	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 0)

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1035151	chr13:50513535-51167850	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1254 gene(s)	inside rSNPs	diseases
2	esv2753964	chr13:50545399-51421199	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
3	esv2753492	chr13:50550081-51461720	Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1256 gene(s)	inside rSNPs	diseases
4	esv2752608	chr13:50550099-51054499	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	1249 gene(s)	inside rSNPs	diseases
5	nsv832608	chr13:50678628-50888413	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
6	nsv1041501	chr13:50683189-50795195	Flanking Active TSS Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
7	esv3404012	chr13:50698476-50701324	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr13:50697200-50700400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr13:50697200-50700400	Active TSS	NHLF	lung
3	chr13:50697400-50700200	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:50697400-50700400	Active TSS	Fetal Brain Female	brain
5	chr13:50697400-50700400	Active TSS	Fetal Muscle Leg	muscle
6	chr13:50697400-50700600	Active TSS	Right Ventricle	heart
7	chr13:50697600-50700200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr13:50697600-50700200	Active TSS	Breast Myoepithelial Primary Cells	Breast
9	chr13:50697600-50700200	Active TSS	Pancreas	Pancrea
10	chr13:50697600-50700400	Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr13:50697600-50700400	Active TSS	Placenta	Placenta
12	chr13:50697600-50700600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr13:50697600-50700600	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr13:50697600-50700600	Active TSS	Aorta	Aorta
15	chr13:50697600-50700600	Active TSS	Lung	lung
16	chr13:50697600-50700800	Active TSS	Esophagus	oesophagus
17	chr13:50697600-50700800	Active TSS	Fetal Muscle Trunk	muscle
18	chr13:50697600-50702000	Active TSS	Psoas Muscle	Psoas
19	chr13:50697600-50702000	Active TSS	Right Atrium	heart
20	chr13:50697600-50702200	Active TSS	Left Ventricle	heart
21	chr13:50697800-50700200	Active TSS	Primary T helper cells PMA-I stimulated	--
22	chr13:50697800-50700200	Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr13:50697800-50700200	Active TSS	Fetal Intestine Large	intestine
24	chr13:50697800-50700200	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr13:50697800-50700400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:50697800-50700400	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr13:50697800-50700400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:50697800-50700400	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr13:50697800-50700400	Active TSS	Rectal Mucosa Donor 29	rectum
30	chr13:50697800-50700400	Active TSS	Small Intestine	intestine
31	chr13:50697800-50700400	Active TSS	Thymus	Thymus
32	chr13:50697800-50700400	Active TSS	NHDF-Ad	bronchial
33	chr13:50697800-50700600	Active TSS	Primary T helper memory cells from peripheral blood 2	blood
34	chr13:50697800-50700600	Active TSS	Primary T helper naive cells from peripheral blood	blood
35	chr13:50697800-50700600	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr13:50697800-50700600	Active TSS	Primary T killer memory cells from peripheral blood	blood
37	chr13:50697800-50700600	Active TSS	Brain Angular Gyrus	brain
38	chr13:50697800-50700600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
39	chr13:50697800-50700600	Active TSS	Rectal Smooth Muscle	rectum
40	chr13:50697800-50700600	Active TSS	Stomach Smooth Muscle	stomach
41	chr13:50697800-50700600	Active TSS	K562	blood
42	chr13:50697800-50700800	Active TSS	Colon Smooth Muscle	Colon
43	chr13:50697800-50700800	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr13:50697800-50700800	Active TSS	Sigmoid Colon	Sigmoid Colon
45	chr13:50697800-50702000	Active TSS	Brain Anterior Caudate	brain
46	chr13:50697800-50702200	Active TSS	Brain Substantia Nigra	brain
47	chr13:50698000-50700200	Active TSS	iPS-15b Cell Line	embryonic stem cell
48	chr13:50698000-50700200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr13:50698000-50700200	Active TSS	Primary monocytes fromperipheralblood	blood
50	chr13:50698000-50700200	Active TSS	Primary T cells fromperipheralblood	blood

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