Variant report

Variant	rs2066590
Chromosome Location	chr13:50701190-50701191
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	POLR2A	chr13:50697801-50703833	H1-neurons	neurons:	n/a	n/a
2	ELF1	chr13:50701118-50701842	GM12878	blood:	n/a	chr13:50701536-50701548
3	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
4	MXI1	chr13:50697635-50701199	IMR90	lung:	n/a	n/a
5	SUZ12	chr13:50700125-50702970	H1-hESC	embryonic stem cell:	n/a	n/a
6	POLR2A	chr13:50701139-50701411	MCF-7	breast:	n/a	n/a
7	CTCF	chr13:50701178-50701218	Spleen_OC	spleen:	n/a	n/a
8	CTBP2	chr13:50699765-50702817	H1-hESC	embryonic stem cell:	n/a	n/a
9	POLR2A	chr13:50697748-50701247	Hela-S3	cervix:	n/a	n/a
10	SUZ12	chr13:50700187-50703150	NT2-D1	testis:	n/a	n/a
11	POLR2A	chr13:50697768-50704046	H1-neurons	neurons:	n/a	n/a
12	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	chr13:50699919..50702491-chr17:57916602..57918837,2	MCF-7	breast:
5	chr13:50569500..50573569-chr13:50696112..50701767,10	K562	blood:
6	chr13:50698913..50701877-chr17:56707826..56709440,2	MCF-7	breast:
7	chr13:50698526..50701372-chr13:50933812..50935948,3	MCF-7	breast:
8	chr13:50698015..50701526-chr13:51100615..51103673,4	MCF-7	breast:
9	chr13:50654073..50663597-chr13:50696674..50702768,25	MCF-7	breast:
10	chr13:50652189..50666968-chr13:50693462..50701392,46	MCF-7	breast:
11	chr13:50696939..50701257-chr13:51483386..51488031,9	K562	blood:
12	chr13:50699976..50701803-chr13:51102949..51104727,2	MCF-7	breast:
13	chr13:50700096..50702357-chr13:50721574..50724200,2	K562	blood:
14	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
ENSG00000136104	Chromatin interaction
ENSG00000199004	Chromatin interaction
ENSG00000176124	Chromatin interaction
ENSG00000231607	Chromatin interaction
ENSG00000204977	Chromatin interaction
ENSG00000229323	Chromatin interaction
ENSG00000233672	Chromatin interaction
ENSG00000264864	Chromatin interaction
ENSG00000223676	Chromatin interaction
ENSG00000212195	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs12876820	1.00[AFR][1000 genomes]
rs1523178	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2812203	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9316484	0.98[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9526636	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9535415	0.91[AMR][1000 genomes];0.91[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
rs2066590	TRIM13	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 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	chr13:50700000-50701400	Flanking Active TSS	Dnd41	blood
10	chr13:50700000-50701600	Flanking Active TSS	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:50700000-50702200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr13:50700000-50702200	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
13	chr13:50700000-50702400	Flanking Active TSS	Primary hematopoietic stem cells	blood
14	chr13:50700000-50702400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr13:50700000-50702400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr13:50700200-50701200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr13:50700200-50701400	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
18	chr13:50700200-50701600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr13:50700200-50701800	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
20	chr13:50700200-50701800	Flanking Bivalent TSS/Enh	NHEK	skin
21	chr13:50700200-50702000	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
22	chr13:50700200-50702000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
23	chr13:50700200-50702000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr13:50700200-50702400	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
25	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr13:50700400-50701200	Flanking Bivalent TSS/Enh	iPS-15b Cell Line	embryonic stem cell
28	chr13:50700400-50701400	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr13:50700400-50701400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
30	chr13:50700400-50701400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr13:50700400-50701400	Weak transcription	Ovary	ovary
32	chr13:50700400-50701600	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
33	chr13:50700400-50701600	Flanking Active TSS	Primary B cells from peripheral blood	blood
34	chr13:50700400-50701600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr13:50700400-50701600	Flanking Active TSS	Duodenum Mucosa	Duodenum
36	chr13:50700400-50701600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
37	chr13:50700400-50701800	Flanking Bivalent TSS/Enh	HUES48 Cell Line	embryonic stem cell
38	chr13:50700400-50701800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
39	chr13:50700400-50702000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
40	chr13:50700400-50702200	Flanking Active TSS	Primary T cells from cord blood	blood
41	chr13:50700400-50702200	Enhancers	Small Intestine	intestine
42	chr13:50700400-50702400	Flanking Bivalent TSS/Enh	Fetal Intestine Small	intestine
43	chr13:50700400-50702400	Flanking Bivalent TSS/Enh	Fetal Thymus	thymus
44	chr13:50700400-50702600	Bivalent/Poised TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr13:50700400-50702800	Flanking Bivalent TSS/Enh	H1 Cell Line	embryonic stem cell
46	chr13:50700600-50701200	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr13:50700600-50701200	Flanking Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
48	chr13:50700600-50701200	Flanking Bivalent TSS/Enh	Fetal Lung	lung
49	chr13:50700600-50701200	Flanking Active TSS	Hela-S3	cervix
50	chr13:50700600-50701400	Bivalent Enhancer	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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