Variant report

Variant	rs9588247
Chromosome Location	chr13:111375571-111375572
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:111370419..111377483-chr13:111379803..111385146,6	MCF-7	breast:

Extended variants
information (count: 46 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1061386	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11618891	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12875067	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1441042	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1441043	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119479	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2165418	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3809344	0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4771707	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4773240	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4773241	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4773244	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61971615	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6492302	0.88[EUR][1000 genomes]
rs6492303	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492304	0.85[EUR][1000 genomes]
rs6492305	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492306	0.86[EUR][1000 genomes]
rs6492308	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7318291	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7319459	0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7330080	0.86[EUR][1000 genomes]
rs7337126	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338458	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs754599	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7984468	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7985098	0.84[EUR][1000 genomes]
rs7986286	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7991766	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9301476	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9515273	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9515274	0.84[EUR][1000 genomes]
rs9521905	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9521909	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521910	0.81[ASN][1000 genomes]
rs9521912	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9521913	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9521914	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs9521915	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9555724	0.88[EUR][1000 genomes]
rs9555726	0.88[EUR][1000 genomes]
rs9559863	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9588247	CARS2	cis	Nerve Tibial	GTEx

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111369200-111376000	Weak transcription	Colon Smooth Muscle	Colon
2	chr13:111369200-111376200	Weak transcription	HSMMtube	muscle
3	chr13:111369200-111381400	Weak transcription	Brain Cingulate Gyrus	brain
4	chr13:111370200-111379000	Weak transcription	HUVEC	blood vessel
5	chr13:111370200-111383400	Weak transcription	Right Atrium	heart
6	chr13:111370400-111379400	Weak transcription	Fetal Kidney	kidney
7	chr13:111370800-111375600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr13:111370800-111375800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr13:111370800-111377800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:111370800-111378000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr13:111370800-111379200	Weak transcription	Psoas Muscle	Psoas
12	chr13:111370800-111380200	Weak transcription	HSMM	muscle
13	chr13:111370800-111380800	Weak transcription	Hela-S3	cervix
14	chr13:111371000-111377800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
15	chr13:111371000-111377800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
16	chr13:111371200-111375600	Strong transcription	Dnd41	blood
17	chr13:111371400-111376400	Strong transcription	Monocytes-CD14+_RO01746	blood
18	chr13:111371600-111377800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
19	chr13:111371800-111376000	Strong transcription	Primary B cells from peripheral blood	blood
20	chr13:111372000-111375600	Strong transcription	Primary monocytes fromperipheralblood	blood
21	chr13:111372200-111376000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr13:111372200-111376200	Strong transcription	Thymus	Thymus
23	chr13:111372200-111376600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr13:111372200-111376600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
25	chr13:111372200-111377400	Weak transcription	Left Ventricle	heart
26	chr13:111372200-111377800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr13:111372200-111378200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:111372200-111379000	Weak transcription	Small Intestine	intestine
29	chr13:111372200-111379600	Weak transcription	NHLF	lung
30	chr13:111372200-111380000	Weak transcription	Gastric	stomach
31	chr13:111372200-111381600	Weak transcription	A549	lung
32	chr13:111372200-111383400	Weak transcription	Esophagus	oesophagus
33	chr13:111372200-111383600	Weak transcription	Aorta	Aorta
34	chr13:111372200-111384200	Weak transcription	Primary hematopoietic stem cells	blood
35	chr13:111372400-111379200	Weak transcription	Lung	lung
36	chr13:111372400-111379200	Weak transcription	Pancreas	Pancrea
37	chr13:111372400-111379200	Weak transcription	Rectal Smooth Muscle	rectum
38	chr13:111372400-111379600	Weak transcription	Brain Substantia Nigra	brain
39	chr13:111372400-111380000	Weak transcription	Colonic Mucosa	Colon
40	chr13:111372400-111381400	Weak transcription	Right Ventricle	heart
41	chr13:111372400-111381600	Weak transcription	Fetal Intestine Small	intestine
42	chr13:111372400-111382000	Weak transcription	Fetal Muscle Trunk	muscle
43	chr13:111372400-111382400	Weak transcription	H9 Cell Line	embryonic stem cell
44	chr13:111372400-111383200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
45	chr13:111372400-111383400	Weak transcription	Rectal Mucosa Donor 31	rectum
46	chr13:111372400-111384200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr13:111372600-111376000	Weak transcription	HepG2	liver
48	chr13:111372600-111376000	Weak transcription	NH-A	brain
49	chr13:111372600-111377000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr13:111372600-111378800	Weak transcription	Primary T cells from cord blood	blood

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