Variant report

Variant	rs436462
Chromosome Location	chr13:111298392-111298393
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:18)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:18 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:111298006-111298486	GM12878	blood:	n/a	n/a
2	POLR2A	chr13:111298192-111298425	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr13:111286846-111300127	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr13:111290793-111300178	K562	blood:	n/a	n/a
5	POLR2A	chr13:111288525-111302316	U87	brain:	n/a	n/a
6	POLR2A	chr13:111298031-111298567	ECC-1	luminal epithelium:	n/a	n/a
7	POLR2A	chr13:111298364-111298401	K562	blood:	n/a	n/a
8	POLR2A	chr13:111296069-111300374	GM12878	blood:	n/a	n/a
9	POLR2A	chr13:111298266-111298480	Hela-S3	cervix:	n/a	n/a
10	POLR2A	chr13:111298252-111298473	K562	blood:	n/a	n/a
11	POLR2A	chr13:111296836-111298595	HL-60	blood:	n/a	n/a
12	EBF1	chr13:111297824-111298746	GM12878	blood:	n/a	chr13:111298040-111298050 chr13:111298039-111298050
13	POLR2A	chr13:111296725-111300096	SK-N-MC	brain:	n/a	n/a
14	CTCF	chr13:111298360-111298510	HCPEpiC	choroid plexus:	n/a	n/a
15	POLR2A	chr13:111295281-111299091	U87	brain:	n/a	n/a
16	POLR2A	chr13:111298265-111298469	HepG2	liver:	n/a	n/a
17	POLR2A	chr13:111295281-111299073	U87	brain:	n/a	n/a
18	POLR2A	chr13:111288564-111302262	U87	brain:	n/a	n/a

No data

(count:7 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111266944..111268705-chr13:111296076..111298471,2	K562	blood:
2	chr13:111295643..111300120-chr13:111365518..111369026,8	MCF-7	breast:
3	chr13:111296887..111299817-chr13:111365376..111368411,4	MCF-7	breast:
4	chr13:111297109..111298768-chr13:111365572..111368457,2	K562	blood:
5	chr13:111297577..111299513-chr13:111565470..111567515,2	MCF-7	breast:
6	chr13:111294769..111302902-chr13:111363368..111369699,14	K562	blood:
7	chr13:111266655..111268705-chr13:111294879..111298471,3	K562	blood:

No data

Variant related genes	Relation type
CARS2	TF binding region
ENSG00000088448	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000153487	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1193458	0.95[CHB][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2119480	0.91[CHB][hapmap]
rs2986322	0.96[YRI][hapmap]
rs369788	0.95[CHB][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs376602	0.95[CHB][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs378399	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs381835	0.96[CHB][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs386109	0.90[YRI][hapmap]
rs401084	0.96[CHB][hapmap];0.82[ASN][1000 genomes]
rs418935	0.95[CHB][hapmap];0.82[ASN][1000 genomes]
rs453757	1.00[CHB][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs4771705	0.91[CHB][hapmap]
rs7998328	0.91[CHB][hapmap]
rs9515266	0.86[CHB][hapmap]
rs9521884	0.91[CHB][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs436462	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs436462	AL139385.1	cis	Muscle Skeletal	GTEx
rs436462	CARS2	cis	brain	BrainEAC
rs436462	CARKD	cis	Muscle Skeletal	GTEx

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	chr13:111287200-111298400	Strong transcription	A549	lung
11	chr13:111287400-111310200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr13:111287800-111309800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr13:111289400-111312000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr13:111289600-111298800	Strong transcription	NHEK	skin
15	chr13:111289600-111310000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr13:111290800-111298400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr13:111293400-111314800	Weak transcription	HUVEC	blood vessel
18	chr13:111294000-111300200	Weak transcription	K562	blood
19	chr13:111294000-111311800	Weak transcription	Fetal Kidney	kidney
20	chr13:111296000-111307200	Weak transcription	Hela-S3	cervix
21	chr13:111296000-111311600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
22	chr13:111296400-111301600	Weak transcription	Aorta	Aorta
23	chr13:111296600-111300600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr13:111296600-111300800	Weak transcription	Esophagus	oesophagus
25	chr13:111296600-111311400	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr13:111296800-111298400	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr13:111296800-111310000	Weak transcription	HUES64 Cell Line	embryonic stem cell
28	chr13:111296800-111310200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr13:111297000-111298400	Genic enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr13:111297000-111298400	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
31	chr13:111297000-111298400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
32	chr13:111297000-111298400	Genic enhancers	Spleen	Spleen
33	chr13:111297000-111298600	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr13:111297000-111300800	Weak transcription	Primary T cells from cord blood	blood
35	chr13:111297000-111301400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr13:111297000-111301800	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr13:111297200-111299400	Weak transcription	Adipose Nuclei	Adipose
38	chr13:111297200-111300600	Weak transcription	Duodenum Smooth Muscle	Duodenum
39	chr13:111297200-111302600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr13:111297200-111302800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
41	chr13:111297200-111307600	Weak transcription	HSMMtube	muscle
42	chr13:111297200-111310200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr13:111297200-111313800	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr13:111297400-111302000	Weak transcription	Primary hematopoietic stem cells	blood
45	chr13:111297400-111302000	Weak transcription	Fetal Lung	lung
46	chr13:111297400-111302800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
47	chr13:111297400-111303000	Weak transcription	HSMM	muscle
48	chr13:111297600-111298600	Strong transcription	Right Ventricle	heart
49	chr13:111297600-111299200	Strong transcription	Fetal Brain Female	brain
50	chr13:111297600-111299600	Strong transcription	Cortex derived primary cultured neurospheres	brain

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