Variant report

Variant	rs2740509
Chromosome Location	chr13:50700824-50700825
allele	C/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	POLR2A	chr13:50700801-50701123	MCF-7	breast:	n/a	n/a
2	POLR2A	chr13:50697492-50700918	HL-60	blood:	n/a	n/a
3	KAP1	chr13:50700341-50701039	HEK293	kidney:	n/a	n/a
4	POLR2A	chr13:50697801-50703833	H1-neurons	neurons:	n/a	n/a
5	SMC3	chr13:50699733-50700869	Hela-S3	cervix:	n/a	n/a
6	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
7	MYC	chr13:50697689-50701139	NB4	blood:	n/a	chr13:50699900-50699909 chr13:50698347-50698357 chr13:50698675-50698684
8	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
9	MXI1	chr13:50697635-50701199	IMR90	lung:	n/a	n/a
10	POLR2A	chr13:50695898-50700883	MCF10A-Er-Src	breast:	n/a	n/a
11	POLR2A	chr13:50696928-50700833	IMR90	lung:	n/a	n/a
12	MTA3	chr13:50699978-50701077	GM12878	blood:	n/a	n/a
13	MXI1	chr13:50697955-50700848	HepG2	liver:	n/a	n/a
14	POLR2A	chr13:50698224-50700936	Raji	blood:	n/a	n/a
15	FOXA2	chr13:50700304-50700929	A549	lung:	n/a	n/a
16	POLR2A	chr13:50697077-50700841	MCF10A-Er-Src	breast:	n/a	n/a
17	ZNF263	chr13:50699894-50700983	HEK293-T-REx	kidney:	n/a	n/a
18	POLR2A	chr13:50697314-50700896	HepG2	liver:	n/a	n/a
19	MAX	chr13:50697665-50700957	NB4	blood:	n/a	chr13:50699900-50699909 chr13:50698347-50698357 chr13:50698675-50698684
20	SUZ12	chr13:50700125-50702970	H1-hESC	embryonic stem cell:	n/a	n/a
21	SMARCB1	chr13:50697955-50700937	Hela-S3	cervix:	n/a	chr13:50698065-50698074
22	FOXA1	chr13:50699463-50700892	HepG2	liver:	n/a	n/a
23	POLR2A	chr13:50697695-50700887	PANC-1	pancreas:	n/a	n/a
24	POLR2A	chr13:50697354-50700892	PBDE	blood:	n/a	n/a
25	POLR2A	chr13:50697647-50701076	HL-60	blood:	n/a	n/a
26	POLR2A	chr13:50699833-50700955	K562	blood:	n/a	n/a
27	MYC	chr13:50699417-50700914	A549	lung:	n/a	chr13:50699900-50699909
28	CTBP2	chr13:50699765-50702817	H1-hESC	embryonic stem cell:	n/a	n/a
29	FOXA1	chr13:50700357-50700858	HepG2	liver:	n/a	n/a
30	POLR2A	chr13:50697681-50701055	NB4	blood:	n/a	n/a
31	POLR2A	chr13:50697748-50701247	Hela-S3	cervix:	n/a	n/a
32	POLR2A	chr13:50696518-50701188	HepG2	liver:	n/a	n/a
33	POLR2A	chr13:50697725-50700970	Hela-S3	cervix:	n/a	n/a
34	SUZ12	chr13:50700187-50703150	NT2-D1	testis:	n/a	n/a
35	MAX	chr13:50699523-50700851	A549	lung:	n/a	chr13:50699900-50699909
36	POLR2A	chr13:50700774-50700931	MCF-7	breast:	n/a	n/a
37	FOXA2	chr13:50700419-50700836	A549	lung:	n/a	n/a
38	POLR2A	chr13:50697768-50704046	H1-neurons	neurons:	n/a	n/a
39	POLR2A	chr13:50697566-50701226	K562	blood:	n/a	n/a

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	chr13:50568991..50573569-chr13:50697831..50701767,8	K562	blood:
4	chr13:50699189..50701054-chr16:1428158..1429695,2	MCF-7	breast:
5	chr13:50699919..50702491-chr17:57916602..57918837,2	MCF-7	breast:
6	chr13:50569500..50573569-chr13:50696112..50701767,10	K562	blood:
7	chr13:50698611..50701082-chr13:51100302..51101813,2	MCF-7	breast:
8	chr13:50698913..50701877-chr17:56707826..56709440,2	MCF-7	breast:
9	chr13:50698526..50701372-chr13:50933812..50935948,3	MCF-7	breast:
10	chr13:50698015..50701526-chr13:51100615..51103673,4	MCF-7	breast:
11	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
12	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:
13	chr13:50696939..50701257-chr13:51483386..51488031,9	K562	blood:
14	chr13:50699976..50701803-chr13:51102949..51104727,2	MCF-7	breast:
15	chr13:50569368..50571479-chr13:50698927..50701104,2	MCF-7	breast:
16	chr13:50700096..50702357-chr13:50721574..50724200,2	K562	blood:
17	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
ENSG00000265529	Chromatin interaction
ENSG00000212195	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000059145	Chromatin interaction
ENSG00000223676	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000136104	Chromatin interaction
ENSG00000229323	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000264864	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1622458	0.93[EUR][1000 genomes]
rs2066581	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2066593	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2066600	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2066603	0.85[EUR][1000 genomes]
rs2760911	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2812203	0.93[ASN][1000 genomes]
rs7318151	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9535414	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9535416	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9740075	0.82[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]

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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2740509	DLEU1	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:50697600-50702000	Active TSS	Psoas Muscle	Psoas
2	chr13:50697600-50702000	Active TSS	Right Atrium	heart
3	chr13:50697600-50702200	Active TSS	Left Ventricle	heart
4	chr13:50697800-50702000	Active TSS	Brain Anterior Caudate	brain
5	chr13:50697800-50702200	Active TSS	Brain Substantia Nigra	brain
6	chr13:50698000-50702000	Active TSS	Brain Hippocampus Middle	brain
7	chr13:50699200-50702400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
8	chr13:50699800-50702200	Flanking Active TSS	Primary B cells from cord blood	blood
9	chr13:50700000-50701000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
10	chr13:50700000-50701400	Flanking Active TSS	Dnd41	blood
11	chr13:50700000-50701600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
12	chr13:50700000-50702200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr13:50700000-50702200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
14	chr13:50700000-50702400	Flanking Active TSS	Primary hematopoietic stem cells	blood
15	chr13:50700000-50702400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr13:50700000-50702400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr13:50700200-50701000	Flanking Active TSS	Primary T helper naive cells fromperipheralblood	blood
18	chr13:50700200-50701000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr13:50700200-50701200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr13:50700200-50701400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
21	chr13:50700200-50701600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
22	chr13:50700200-50701800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
23	chr13:50700200-50701800	Flanking Bivalent TSS/Enh	NHEK	skin
24	chr13:50700200-50702000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
25	chr13:50700200-50702000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
26	chr13:50700200-50702000	Flanking Active TSS	Adipose Nuclei	Adipose
27	chr13:50700200-50702400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
28	chr13:50700400-50701000	Flanking Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr13:50700400-50701000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr13:50700400-50701000	Flanking Active TSS	Brain Cingulate Gyrus	brain
31	chr13:50700400-50701000	Flanking Active TSS	Fetal Brain Female	brain
32	chr13:50700400-50701000	Flanking Active TSS	Fetal Heart	heart
33	chr13:50700400-50701000	Flanking Active TSS	Fetal Muscle Leg	muscle
34	chr13:50700400-50701000	Flanking Active TSS	Placenta	Placenta
35	chr13:50700400-50701000	Weak transcription	Gastric	stomach
36	chr13:50700400-50701000	Flanking Active TSS	Osteobl	bone
37	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
38	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
40	chr13:50700400-50701400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr13:50700400-50701400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
42	chr13:50700400-50701400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr13:50700400-50701400	Weak transcription	Ovary	ovary
44	chr13:50700400-50701600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
45	chr13:50700400-50701600	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr13:50700400-50701600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
47	chr13:50700400-50701600	Flanking Active TSS	Duodenum Mucosa	Duodenum
48	chr13:50700400-50701600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
49	chr13:50700400-50701800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
50	chr13:50700400-50701800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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