Variant report

Variant	rs754599
Chromosome Location	chr13:111354788-111354789
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr13:111354377..111357375-chr13:111522032..111524115,2	K562	blood:
2	chr13:111354215..111355804-chr13:111356852..111360371,4	MCF-7	breast:
3	chr13:111328169..111330528-chr13:111354350..111356160,2	K562	blood:
4	chr13:111341286..111343605-chr13:111352948..111355342,2	K562	blood:

Variant related genes	Relation type
ENSG00000134905	Chromatin interaction
ENSG00000255874	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs1061386	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11618891	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12875067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1441042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1441043	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2083568	0.81[AMR][1000 genomes]
rs2119479	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.82[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2165418	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289461	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3809344	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3818496	0.91[EUR][1000 genomes]
rs4771707	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773240	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4773244	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61971615	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492302	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6492303	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6492304	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492305	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6492306	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492308	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7318291	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7319459	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7330080	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7337126	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7338458	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7984468	0.88[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7985098	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7986286	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7991766	0.87[EUR][1000 genomes]
rs9301476	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9515273	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9515274	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9521905	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9521909	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9521910	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9521913	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9521914	0.85[EUR][1000 genomes]
rs9521915	0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9555724	1.00[CEU][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9555726	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9559863	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9588247	0.88[EUR][1000 genomes];0.91[ASN][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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs754599	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs754599	CARS2	cis	Nerve Tibial	GTEx
rs754599	CARKD	cis	parietal	SCAN
rs754599	CARS2	cis	parietal	SCAN

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	chr13:111327800-111355000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr13:111328000-111354800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr13:111328000-111356600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr13:111328400-111355600	Strong transcription	NHEK	skin
6	chr13:111329000-111354800	Strong transcription	Fetal Stomach	stomach
7	chr13:111330000-111355000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr13:111330400-111355200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr13:111332600-111356600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
10	chr13:111337000-111355000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr13:111339600-111355400	Weak transcription	Small Intestine	intestine
12	chr13:111343200-111354800	Weak transcription	Psoas Muscle	Psoas
13	chr13:111343200-111355000	Weak transcription	Right Atrium	heart
14	chr13:111344800-111356200	Strong transcription	Duodenum Mucosa	Duodenum
15	chr13:111345600-111355000	Strong transcription	Fetal Brain Female	brain
16	chr13:111346000-111355800	Strong transcription	Rectal Mucosa Donor 29	rectum
17	chr13:111347000-111355400	Strong transcription	Adipose Nuclei	Adipose
18	chr13:111347200-111355000	Strong transcription	HUES6 Cell Line	embryonic stem cell
19	chr13:111347200-111355000	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr13:111347400-111355000	Strong transcription	Ovary	ovary
21	chr13:111348200-111354800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
22	chr13:111348800-111354800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
23	chr13:111348800-111354800	Strong transcription	Placenta	Placenta
24	chr13:111349000-111355200	Strong transcription	Fetal Intestine Large	intestine
25	chr13:111349200-111355000	Strong transcription	Lung	lung
26	chr13:111349200-111355600	Strong transcription	Fetal Intestine Small	intestine
27	chr13:111349200-111355800	Strong transcription	Sigmoid Colon	Sigmoid Colon
28	chr13:111349400-111356000	Strong transcription	Primary T cells from cord blood	blood
29	chr13:111350000-111355000	Strong transcription	HepG2	liver
30	chr13:111350800-111355600	Strong transcription	H9 Cell Line	embryonic stem cell
31	chr13:111351400-111354800	Strong transcription	Fetal Muscle Trunk	muscle
32	chr13:111351600-111354800	Strong transcription	Brain Inferior Temporal Lobe	brain
33	chr13:111352000-111355000	Weak transcription	Fetal Brain Male	brain
34	chr13:111352000-111355200	Strong transcription	Primary B cells from cord blood	blood
35	chr13:111352000-111356400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr13:111352200-111355600	Strong transcription	Primary B cells from peripheral blood	blood
37	chr13:111352200-111356200	Strong transcription	Primary hematopoietic stem cells	blood
38	chr13:111352400-111354800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr13:111352400-111354800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr13:111352400-111356400	Genic enhancers	Primary monocytes fromperipheralblood	blood
41	chr13:111352400-111357200	Weak transcription	HUVEC	blood vessel
42	chr13:111352600-111354800	Strong transcription	GM12878-XiMat	blood
43	chr13:111352600-111355000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr13:111352600-111355000	Weak transcription	Stomach Mucosa	stomach
45	chr13:111352600-111355400	Weak transcription	Pancreatic Islets	Pancreatic Islet
46	chr13:111352800-111354800	Weak transcription	A549	lung
47	chr13:111352800-111355800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr13:111353000-111354800	Strong transcription	Monocytes-CD14+_RO01746	blood
49	chr13:111353200-111355000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr13:111353200-111355000	Weak transcription	Pancreas	Pancrea

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