Variant report

Variant	rs6492304
Chromosome Location	chr13:111356964-111356965
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111354377..111357375-chr13:111522032..111524115,2	K562	blood:

Variant related genes	Relation type
ENSG00000255874	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs1061386	0.85[EUR][1000 genomes]
rs11618891	0.83[EUR][1000 genomes]
rs12875067	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1441042	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1441043	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2119479	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2165418	0.82[EUR][1000 genomes]
rs2289461	0.84[EUR][1000 genomes]
rs3809344	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3818496	0.90[EUR][1000 genomes]
rs4771707	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4773240	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4773241	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4773244	0.81[EUR][1000 genomes]
rs61971615	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492302	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6492303	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6492305	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6492306	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6492308	0.83[EUR][1000 genomes]
rs7318291	0.87[EUR][1000 genomes]
rs7319459	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7330080	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7337126	0.85[EUR][1000 genomes]
rs7338458	0.85[EUR][1000 genomes]
rs754599	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7984468	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7985098	0.89[EUR][1000 genomes]
rs7986286	0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7991766	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9301476	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9515273	0.82[EUR][1000 genomes]
rs9515274	0.88[EUR][1000 genomes]
rs9521905	0.87[EUR][1000 genomes]
rs9521909	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9521910	0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs9521913	0.82[EUR][1000 genomes]
rs9521914	0.82[EUR][1000 genomes]
rs9521915	0.83[EUR][1000 genomes]
rs9555724	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9555726	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9559863	0.84[EUR][1000 genomes]
rs9588247	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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	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
4	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
5	nsv901014	chr13:111302922-111380684	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	197 gene(s)	inside rSNPs	diseases
6	esv1818465	chr13:111329426-111360585	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
7	esv1820532	chr13:111329426-111360585	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers 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	8 gene(s)	inside rSNPs	diseases
8	esv1823336	chr13:111329535-111360585	Weak transcription Genic enhancers Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	diseases
9	nsv519282	chr13:111343888-111360585	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a
10	esv3345776	chr13:111356851-111361549	Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	8 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6492304	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs6492304	CARS2	cis	Nerve Tibial	GTEx

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111312800-111357400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr13:111352400-111357200	Weak transcription	HUVEC	blood vessel
3	chr13:111353200-111357200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr13:111353400-111357200	Weak transcription	Brain Anterior Caudate	brain
5	chr13:111353400-111357600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:111353600-111357200	Weak transcription	Brain Substantia Nigra	brain
7	chr13:111353800-111357200	Weak transcription	Colonic Mucosa	Colon
8	chr13:111354000-111357200	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:111354200-111357200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr13:111354200-111357200	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr13:111354200-111357200	Weak transcription	Liver	Liver
12	chr13:111354200-111357400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr13:111354200-111357400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr13:111354400-111357400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr13:111354400-111357600	Enhancers	Primary neutrophils fromperipheralblood	blood
16	chr13:111354600-111357400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
17	chr13:111354600-111357400	Enhancers	Fetal Heart	heart
18	chr13:111354800-111357200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
19	chr13:111355000-111357000	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:111355000-111357600	Enhancers	Stomach Mucosa	stomach
21	chr13:111355400-111357000	Weak transcription	Adipose Nuclei	Adipose
22	chr13:111355400-111357200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr13:111355400-111357200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:111355600-111357200	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr13:111355600-111357200	Weak transcription	Cortex derived primary cultured neurospheres	brain
26	chr13:111355600-111357400	Weak transcription	Brain Angular Gyrus	brain
27	chr13:111355600-111357800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr13:111355600-111357800	Weak transcription	Aorta	Aorta
29	chr13:111355600-111358000	Weak transcription	Small Intestine	intestine
30	chr13:111355800-111357000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr13:111355800-111357200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
32	chr13:111355800-111357200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr13:111355800-111357200	Weak transcription	Fetal Brain Male	brain
34	chr13:111355800-111357200	Weak transcription	Rectal Mucosa Donor 29	rectum
35	chr13:111355800-111357200	Enhancers	Skeletal Muscle Female	skeletal muscle
36	chr13:111355800-111357200	Enhancers	HepG2	liver
37	chr13:111355800-111357400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
38	chr13:111355800-111357400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr13:111355800-111357400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
40	chr13:111355800-111357400	Enhancers	Primary T helper cells PMA-I stimulated	--
41	chr13:111355800-111357400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr13:111355800-111357400	Weak transcription	Left Ventricle	heart
43	chr13:111355800-111357400	Weak transcription	Right Ventricle	heart
44	chr13:111355800-111357600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
45	chr13:111355800-111357600	Weak transcription	Right Atrium	heart
46	chr13:111355800-111358000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr13:111355800-111358000	Weak transcription	Gastric	stomach
48	chr13:111356000-111357200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr13:111356000-111357200	Weak transcription	Fetal Brain Female	brain
50	chr13:111356000-111357200	Enhancers	Skeletal Muscle Male	skeletal muscle

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