Variant report

Variant	rs450565
Chromosome Location	chr13:111299061-111299062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:15)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:15 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:111286846-111300127	Hela-S3	cervix:	n/a	n/a
2	POLR2A	chr13:111290793-111300178	K562	blood:	n/a	n/a
3	POLR2A	chr13:111288525-111302316	U87	brain:	n/a	n/a
4	POLR2A	chr13:111299008-111299195	H1-hESC	embryonic stem cell:	n/a	n/a
5	POLR2A	chr13:111296069-111300374	GM12878	blood:	n/a	n/a
6	POLR2A	chr13:111298800-111299119	GM12891	blood:	n/a	n/a
7	POLR2A	chr13:111298835-111299232	GM12892	blood:	n/a	n/a
8	POLR2A	chr13:111298994-111299848	GM12878	blood:	n/a	n/a
9	POLR2A	chr13:111298960-111299251	HepG2	liver:	n/a	n/a
10	POLR2A	chr13:111296725-111300096	SK-N-MC	brain:	n/a	n/a
11	POLR2A	chr13:111298947-111300024	HL-60	blood:	n/a	n/a
12	POLR2A	chr13:111299028-111299279	K562	blood:	n/a	n/a
13	POLR2A	chr13:111295281-111299091	U87	brain:	n/a	n/a
14	POLR2A	chr13:111295281-111299073	U87	brain:	n/a	n/a
15	POLR2A	chr13:111288564-111302262	U87	brain:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111295643..111300120-chr13:111365518..111369026,8	MCF-7	breast:
2	chr13:111296887..111299817-chr13:111365376..111368411,4	MCF-7	breast:
3	chr13:111297577..111299513-chr13:111565470..111567515,2	MCF-7	breast:
4	chr13:111294769..111302902-chr13:111363368..111369699,14	K562	blood:
5	chr13:111280819..111283163-chr13:111298869..111301563,3	K562	blood:

No data

Variant related genes	Relation type
CARS2	TF binding region
ENSG00000088448	Chromatin interaction
ENSG00000153487	Chromatin interaction
ENSG00000134905	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs410049	0.83[YRI][hapmap]
rs440500	0.83[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1044234	chr13:111143053-111370580	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	216 gene(s)	inside rSNPs	diseases
2	nsv949634	chr13:111151460-111582996	Genic enhancers Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	245 gene(s)	inside rSNPs	diseases
3	nsv1053922	chr13:111167764-111330876	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
4	nsv1043849	chr13:111167764-111340418	Bivalent Enhancer Weak transcription Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
5	nsv541924	chr13:111167764-111340418	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS 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
6	nsv1036160	chr13:111167764-111347308	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
7	nsv541925	chr13:111167764-111347308	Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS 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
8	nsv901012	chr13:111220842-111340342	Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Strong transcription Enhancers Genic enhancers Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	nsv1044340	chr13:111234073-111692994	Bivalent Enhancer Genic enhancers Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
10	nsv563124	chr13:111261267-111300943	Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
11	nsv1048700	chr13:111265350-111658617	Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	240 gene(s)	inside rSNPs	diseases
12	nsv456120	chr13:111280002-111309617	Strong transcription Weak transcription Genic enhancers Flanking Active TSS Enhancers 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	n/a
13	nsv563125	chr13:111280002-111309617	Strong transcription Genic enhancers Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	n/a
14	nsv1042232	chr13:111282123-111348475	Weak transcription Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
15	nsv901013	chr13:111291192-111340342	ZNF genes & repeats Enhancers Strong transcription Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs450565	SOX1	cis	parietal	SCAN
rs450565	CARKD	cis	parietal	SCAN
rs450565	CARS2	cis	lymphoblastoid	seeQTL
rs450565	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs450565	CARS2	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111280800-111328600	Weak transcription	Psoas Muscle	Psoas
2	chr13:111282000-111309600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr13:111282800-111310000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr13:111286200-111299600	Strong transcription	Placenta	Placenta
5	chr13:111286200-111308400	Strong transcription	Dnd41	blood
6	chr13:111286400-111299800	Strong transcription	HepG2	liver
7	chr13:111286400-111300400	Strong transcription	Thymus	Thymus
8	chr13:111286400-111308200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:111286800-111309400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr13:111287400-111310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr13:111287800-111309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr13:111289400-111312000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:111289600-111310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr13:111293400-111314800	Weak transcription	HUVEC	blood vessel
15	chr13:111294000-111300200	Weak transcription	K562	blood
16	chr13:111294000-111311800	Weak transcription	Fetal Kidney	kidney
17	chr13:111296000-111307200	Weak transcription	Hela-S3	cervix
18	chr13:111296000-111311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr13:111296400-111301600	Weak transcription	Aorta	Aorta
20	chr13:111296600-111300600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr13:111296600-111300800	Weak transcription	Esophagus	oesophagus
22	chr13:111296600-111311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr13:111296800-111310000	Weak transcription	HUES64 Cell Line	embryonic stem cell
24	chr13:111296800-111310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:111297000-111300800	Weak transcription	Primary T cells from cord blood	blood
26	chr13:111297000-111301400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr13:111297000-111301800	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr13:111297200-111299400	Weak transcription	Adipose Nuclei	Adipose
29	chr13:111297200-111300600	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr13:111297200-111302600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr13:111297200-111302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr13:111297200-111307600	Weak transcription	HSMMtube	muscle
33	chr13:111297200-111310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
34	chr13:111297200-111313800	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr13:111297400-111302000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr13:111297400-111302000	Weak transcription	Fetal Lung	lung
37	chr13:111297400-111302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr13:111297400-111303000	Weak transcription	HSMM	muscle
39	chr13:111297600-111299200	Strong transcription	Fetal Brain Female	brain
40	chr13:111297600-111299600	Strong transcription	Cortex derived primary cultured neurospheres	brain
41	chr13:111297600-111299800	Genic enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr13:111297600-111299800	Strong transcription	Sigmoid Colon	Sigmoid Colon
43	chr13:111297600-111300400	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
44	chr13:111297600-111301200	Weak transcription	Fetal Brain Male	brain
45	chr13:111297600-111301400	Weak transcription	Left Ventricle	heart
46	chr13:111297600-111307600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
47	chr13:111297600-111310000	Strong transcription	Fetal Intestine Small	intestine
48	chr13:111297600-111314400	Strong transcription	Fetal Intestine Large	intestine
49	chr13:111297800-111299200	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr13:111297800-111299400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--

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