Variant report

Variant	rs9555724
Chromosome Location	chr13:111354110-111354111
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	chr13:111340758..111343844-chr13:111351055..111354448,3	K562	blood:
2	chr13:111341286..111343605-chr13:111352948..111355342,2	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs1061386	0.88[EUR][1000 genomes]
rs11618891	0.85[EUR][1000 genomes]
rs12875067	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1441042	1.00[CEU][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1441043	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2083568	0.87[AMR][1000 genomes]
rs2119479	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2119480	0.89[MKK][hapmap]
rs2165418	0.85[EUR][1000 genomes]
rs2289461	0.84[EUR][1000 genomes]
rs2986322	0.93[CHB][hapmap];0.83[JPT][hapmap]
rs330571	0.93[CHB][hapmap]
rs369676	0.93[CHB][hapmap]
rs3809344	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs3818496	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs386109	0.93[CHB][hapmap];0.89[JPT][hapmap]
rs389656	0.93[CHB][hapmap];0.85[CHD][hapmap];0.81[GIH][hapmap];0.94[JPT][hapmap]
rs410049	0.93[CHB][hapmap];0.85[CHD][hapmap];0.94[JPT][hapmap]
rs416552	0.89[CHB][hapmap];0.94[JPT][hapmap]
rs440500	0.93[CHB][hapmap];0.94[JPT][hapmap]
rs4771707	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4773240	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4773241	1.00[CEU][hapmap];0.85[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4773244	0.84[EUR][1000 genomes]
rs61971615	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6492302	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492303	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6492304	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492305	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6492306	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492308	0.86[EUR][1000 genomes]
rs6492310	0.82[AMR][1000 genomes]
rs7318291	0.90[EUR][1000 genomes]
rs7319459	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7330080	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7337126	0.88[EUR][1000 genomes]
rs7338458	0.88[EUR][1000 genomes]
rs754599	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7984468	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7985098	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7986286	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7991766	0.86[EUR][1000 genomes]
rs8000294	0.87[CHB][hapmap];0.94[JPT][hapmap]
rs9301476	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9515266	0.82[MKK][hapmap]
rs9515273	0.85[EUR][1000 genomes]
rs9515274	0.80[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9521905	0.90[EUR][1000 genomes]
rs9521909	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9521910	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs9521913	0.85[EUR][1000 genomes]
rs9521914	0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9521915	0.85[EUR][1000 genomes]
rs9555726	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9559863	0.87[EUR][1000 genomes]
rs9588247	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 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

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs9555724	CARS2	cis	Nerve Tibial	GTEx
rs9555724	CARKD	cis	parietal	SCAN
rs9555724	CARS2	cis	Esophagus Muscularis	GTEx
rs9555724	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs9555724	CARS2	cis	parietal	SCAN
rs9555724	FLJ12118	cis	multi-tissue	Pritchard
rs9555724	CARS2	cis	lymphoblastoid	seeQTL

Chromatin state (count:126 , 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	chr13:111319800-111354600	Weak transcription	Fetal Heart	heart
3	chr13:111327800-111355000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr13:111328000-111354800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr13:111328000-111356600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr13:111328400-111355600	Strong transcription	NHEK	skin
7	chr13:111329000-111354800	Strong transcription	Fetal Stomach	stomach
8	chr13:111330000-111355000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr13:111330400-111355200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr13:111332600-111356600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
11	chr13:111337000-111355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr13:111339400-111354600	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr13:111339600-111355400	Weak transcription	Small Intestine	intestine
14	chr13:111343200-111354800	Weak transcription	Psoas Muscle	Psoas
15	chr13:111343200-111355000	Weak transcription	Right Atrium	heart
16	chr13:111344800-111356200	Strong transcription	Duodenum Mucosa	Duodenum
17	chr13:111345400-111354400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr13:111345400-111354400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr13:111345400-111354600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr13:111345600-111354200	Strong transcription	Liver	Liver
21	chr13:111345600-111355000	Strong transcription	Fetal Brain Female	brain
22	chr13:111345800-111354400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr13:111346000-111354600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr13:111346000-111355800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr13:111346600-111354600	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr13:111347000-111354200	Strong transcription	HUES48 Cell Line	embryonic stem cell
27	chr13:111347000-111354400	Strong transcription	Fetal Thymus	thymus
28	chr13:111347000-111354400	Strong transcription	Osteobl	bone
29	chr13:111347000-111355400	Strong transcription	Adipose Nuclei	Adipose
30	chr13:111347200-111354600	Strong transcription	Dnd41	blood
31	chr13:111347200-111355000	Strong transcription	HUES6 Cell Line	embryonic stem cell
32	chr13:111347200-111355000	Strong transcription	HUES64 Cell Line	embryonic stem cell
33	chr13:111347400-111355000	Strong transcription	Ovary	ovary
34	chr13:111348000-111354400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr13:111348200-111354800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr13:111348800-111354200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
37	chr13:111348800-111354600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
38	chr13:111348800-111354600	Strong transcription	HMEC	breast
39	chr13:111348800-111354800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
40	chr13:111348800-111354800	Strong transcription	Placenta	Placenta
41	chr13:111349000-111354200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr13:111349000-111354400	Strong transcription	Fetal Lung	lung
43	chr13:111349000-111354400	Strong transcription	NHDF-Ad	bronchial
44	chr13:111349000-111354600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr13:111349000-111355200	Strong transcription	Fetal Intestine Large	intestine
46	chr13:111349200-111354600	Strong transcription	Brain Germinal Matrix	brain
47	chr13:111349200-111355000	Strong transcription	Lung	lung
48	chr13:111349200-111355600	Strong transcription	Fetal Intestine Small	intestine
49	chr13:111349200-111355800	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr13:111349400-111354200	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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