Variant report

Variant	rs9555726
Chromosome Location	chr13:111368316-111368317
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr13:111367497-111368567	GM12878	blood:	n/a	n/a
2	REST	chr13:111368176-111368358	A549	lung:	n/a	n/a
3	TAF1	chr13:111367479-111368414	H1-hESC	embryonic stem cell:	n/a	n/a
4	SP1	chr13:111367386-111368414	A549	lung:	n/a	chr13:111367914-111367925
5	GATA1	chr13:111367155-111368801	PBDE	blood:	n/a	chr13:111367646-111367655
6	YY1	chr13:111367858-111368573	HepG2	liver:	n/a	n/a
7	CTCFL	chr13:111368263-111368449	K562	blood:	n/a	n/a
8	POLR2A	chr13:111367107-111368449	SK-N-MC	brain:	n/a	n/a
9	POLR2A	chr13:111368117-111368425	HepG2	liver:	n/a	n/a
10	CTCF	chr13:111368269-111368390	SK-N-SH_RA	brain:	n/a	n/a
11	RAD21	chr13:111368102-111368426	HepG2	liver:	n/a	n/a
12	FOXM1	chr13:111367288-111368447	GM12878	blood:	n/a	n/a
13	BHLHE40	chr13:111367301-111368648	GM12878	blood:	n/a	chr13:111368522-111368538
14	TAF1	chr13:111367951-111368372	K562	blood:	n/a	n/a
15	CTCF	chr13:111368166-111368575	IMR90	lung:	n/a	n/a
16	POLR2A	chr13:111367015-111368511	HUVEC	blood vessel:	n/a	n/a
17	RCOR1	chr13:111367264-111368382	K562	blood:	n/a	n/a
18	SP2	chr13:111367471-111368331	HepG2	liver:	n/a	chr13:111367915-111367930
19	NFATC1	chr13:111367290-111368428	GM12878	blood:	n/a	n/a
20	TCF7L2	chr13:111368240-111368667	PANC-1	pancreas:	n/a	chr13:111368488-111368502 chr13:111368490-111368499
21	REST	chr13:111368276-111368469	PANC-1	pancreas:	n/a	chr13:111368417-111368430 chr13:111368414-111368423 chr13:111368412-111368420 chr13:111368414-111368434 chr13:111368446-111368459
22	SMC3	chr13:111368222-111368556	GM12878	blood:	n/a	n/a
23	HDAC2	chr13:111368142-111368418	K562	blood:	n/a	n/a
24	POLR2A	chr13:111363953-111368530	HUVEC	blood vessel:	n/a	n/a
25	MAX	chr13:111367849-111368812	K562	blood:	n/a	n/a
26	CTCF	chr13:111368260-111368410	Hela-S3	cervix:	n/a	n/a
27	HCFC1	chr13:111363852-111369388	Hela-S3	cervix:	n/a	n/a
28	SIN3A	chr13:111367331-111368609	GM12878	blood:	n/a	chr13:111368414-111368427 chr13:111368413-111368421
29	POLR2A	chr13:111367178-111368466	GM12892	blood:	n/a	n/a
30	CHD2	chr13:111366731-111368786	Hela-S3	cervix:	n/a	chr13:111366785-111366792 chr13:111368525-111368535
31	CTCF	chr13:111368280-111368430	RPTEC	kidney:	n/a	n/a
32	CHD1	chr13:111368208-111369220	H1-hESC	embryonic stem cell:	n/a	chr13:111368525-111368535
33	CREB1	chr13:111367220-111368610	H1-hESC	embryonic stem cell:	n/a	n/a
34	HEY1	chr13:111366987-111368399	HepG2	liver:	n/a	chr13:111367183-111367198
35	CTCF	chr13:111368280-111368430	HEEpiC	esophagus:	n/a	n/a
36	E2F4	chr13:111367159-111368354	MCF10A-Er-Src	breast:	n/a	chr13:111367183-111367193 chr13:111367332-111367344 chr13:111367332-111367341 chr13:111367368-111367377
37	CTCF	chr13:111368260-111368410	HCPEpiC	choroid plexus:	n/a	n/a
38	POLR2A	chr13:111367246-111368458	GM10847	blood:	n/a	n/a
39	ELF1	chr13:111366238-111368717	GM12878	blood:	n/a	chr13:111366324-111366336 chr13:111366732-111366744 chr13:111366323-111366332 chr13:111367181-111367193 chr13:111367759-111367771
40	RELA	chr13:111367307-111368812	GM10847	blood:	n/a	n/a
41	MYC	chr13:111363992-111368746	NB4	blood:	n/a	chr13:111367187-111367197
42	CTCF	chr13:111368279-111368437	GM19239	blood:	n/a	n/a
43	BRCA1	chr13:111367358-111368420	Hela-S3	cervix:	n/a	n/a
44	CTCF	chr13:111368280-111368430	GM12871	blood:	n/a	n/a
45	MAX	chr13:111367165-111368620	ECC-1	luminal epithelium:	n/a	chr13:111367187-111367197
46	TBP	chr13:111367309-111368394	HepG2	liver:	n/a	n/a
47	ESRRA	chr13:111363902-111368825	GM12878	blood:	n/a	chr13:111367521-111367537 chr13:111368738-111368756 chr13:111366821-111366834
48	TAF1	chr13:111368081-111368374	PFSK-1	brain:	n/a	n/a
49	REST	chr13:111368007-111368359	HepG2	liver:	n/a	n/a
50	POLR2A	chr13:111367073-111368486	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr13:111364046..111369200-chr13:111563217..111572060,23	MCF-7	breast:
2	chr13:111366242..111369169-chr9:123638760..123640480,2	K562	blood:
3	chr13:111158122..111160358-chr13:111366408..111368725,2	MCF-7	breast:
4	chr13:111368227..111372332-chr13:111523767..111528470,4	MCF-7	breast:
5	chr13:111367737..111368547-chr2:86850388..86850983,2	Hela-S3	cervix:
6	chr13:111158296..111161279-chr13:111366588..111368622,2	K562	blood:
7	chr13:52026611..52027282-chr13:111367415..111368502,3	Hela-S3	cervix:
8	chr13:111362764..111370771-chr13:111560775..111570046,21	K562	blood:
9	chr13:111367825..111368471-chr5:179125002..179125560,2	Hela-S3	cervix:
10	chr13:111367845..111368764-chr15:41708721..41709435,2	Hela-S3	cervix:
11	chr13:111368245..111369754-chr13:111427344..111430230,2	K562	blood:
12	chr13:111362818..111369538-chr13:111519409..111528258,26	K562	blood:
13	chr13:111367559..111368502-chr4:17812401..17813343,2	Hela-S3	cervix:
14	chr13:111296887..111299817-chr13:111365376..111368411,4	MCF-7	breast:
15	chr13:111295643..111300120-chr13:111365518..111369026,8	MCF-7	breast:
16	chr13:111366177..111368396-chr13:111465118..111467461,3	K562	blood:
17	chr13:111365767..111368359-chr13:111545152..111547913,2	K562	blood:
18	chr13:111294769..111302902-chr13:111363368..111369699,14	K562	blood:
19	chr13:111297109..111298768-chr13:111365572..111368457,2	K562	blood:
20	chr13:111266965..111271727-chr13:111364973..111369025,9	MCF-7	breast:
21	chr13:111362370..111368494-chr13:111564438..111569891,17	K562	blood:
22	chr13:111158284..111162693-chr13:111363847..111368622,9	K562	blood:
23	chr13:111212473..111215656-chr13:111365341..111368678,3	K562	blood:
24	chr13:111367532..111368398-chr7:35734643..35735368,2	Hela-S3	cervix:
25	chr13:111367593..111368509-chr19:40696817..40697667,2	HCT-116	colon:
26	chr13:111211605..111215710-chr13:111363534..111368936,10	MCF-7	breast:
27	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:
28	chr13:111266737..111268751-chr13:111366724..111368921,2	K562	blood:
29	chr13:111367943..111368809-chr13:111471498..111472219,2	K562	blood:
30	chr13:111364470..111369495-chr13:111465123..111470179,9	MCF-7	breast:
31	chr13:111364196..111369437-chr13:111520146..111525538,15	K562	blood:
32	chr13:111368245..111370564-chr13:111427344..111430230,3	K562	blood:
33	chr13:111363576..111369085-chr13:111458761..111470393,19	MCF-7	breast:

Variant related genes	Relation type
CARS2	TF binding region
ENSG00000255874	Chromatin interaction
ENSG00000088448	Chromatin interaction
ENSG00000119403	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000137815	Chromatin interaction
ENSG00000109805	Chromatin interaction
ENSG00000259831	Chromatin interaction
ENSG00000102786	Chromatin interaction
ENSG00000122557	Chromatin interaction
ENSG00000271122	Chromatin interaction
ENSG00000134871	Chromatin interaction
ENSG00000130758	Chromatin interaction
ENSG00000239305	Chromatin interaction
ENSG00000127022	Chromatin interaction
ENSG00000232814	Chromatin interaction
ENSG00000139832	Chromatin interaction

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:45)

rs_ID	r²[population]
rs1061386	0.88[EUR][1000 genomes]
rs11618891	0.85[EUR][1000 genomes]
rs12875067	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1441042	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1441043	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2083568	0.91[AMR][1000 genomes]
rs2119479	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2165418	0.85[EUR][1000 genomes]
rs2289461	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3809344	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs3818496	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4771707	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4773240	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4773241	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4773244	0.84[EUR][1000 genomes]
rs61971615	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6492302	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6492303	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492304	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6492305	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6492306	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6492308	0.86[EUR][1000 genomes]
rs6492310	0.87[AMR][1000 genomes]
rs7318291	0.88[EUR][1000 genomes]
rs7319459	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7330080	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7337126	0.88[EUR][1000 genomes]
rs7338458	0.88[EUR][1000 genomes]
rs754599	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7984468	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7985098	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7986286	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7991766	0.86[EUR][1000 genomes]
rs9301476	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9515273	0.85[EUR][1000 genomes]
rs9515274	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9521905	0.88[EUR][1000 genomes]
rs9521909	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9521910	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9521913	0.85[EUR][1000 genomes]
rs9521914	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9521915	0.85[EUR][1000 genomes]
rs9555724	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:5 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9555726	CARS2	Cis_1M	lymphoblastoid	RTeQTL
rs9555726	CARS2	cis	Esophagus Muscularis	GTEx
rs9555726	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	chr13:111363600-111369000	Active TSS	HUES64 Cell Line	embryonic stem cell
2	chr13:111363600-111369000	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr13:111363600-111370000	Active TSS	HUES6 Cell Line	embryonic stem cell
4	chr13:111363600-111370000	Active TSS	K562	blood
5	chr13:111363600-111370400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr13:111363600-111370800	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
7	chr13:111363800-111368600	Active TSS	Fetal Brain Female	brain
8	chr13:111363800-111368800	Bivalent/Poised TSS	HepG2	liver
9	chr13:111363800-111369000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr13:111363800-111369000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr13:111363800-111369400	Active TSS	Right Ventricle	heart
12	chr13:111363800-111369600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr13:111363800-111369800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:111363800-111369800	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr13:111363800-111369800	Active TSS	Pancreatic Islets	Pancreatic Islet
16	chr13:111363800-111369800	Active TSS	Psoas Muscle	Psoas
17	chr13:111363800-111370200	Active TSS	H9 Cell Line	embryonic stem cell
18	chr13:111363800-111370400	Active TSS	ES-I3 Cell Line	embryonic stem cell
19	chr13:111363800-111370600	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr13:111363800-111370800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr13:111364000-111369000	Active TSS	Esophagus	oesophagus
22	chr13:111364000-111369200	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr13:111364000-111369200	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
24	chr13:111364000-111369200	Active TSS	Fetal Muscle Trunk	muscle
25	chr13:111364000-111369200	Active TSS	Left Ventricle	heart
26	chr13:111364000-111369600	Active TSS	HUES48 Cell Line	embryonic stem cell
27	chr13:111364000-111370200	Active TSS	iPS-18 Cell Line	embryonic stem cell
28	chr13:111364000-111370200	Active TSS	Colonic Mucosa	Colon
29	chr13:111364000-111370200	Active TSS	Fetal Intestine Large	intestine
30	chr13:111364000-111370200	Active TSS	Fetal Intestine Small	intestine
31	chr13:111364000-111370400	Active TSS	H1 Cell Line	embryonic stem cell
32	chr13:111364200-111368600	Active TSS	Primary T killer memory cells from peripheral blood	blood
33	chr13:111364200-111368600	Active TSS	Liver	Liver
34	chr13:111364200-111368600	Active TSS	Brain Inferior Temporal Lobe	brain
35	chr13:111364200-111368600	Active TSS	Thymus	Thymus
36	chr13:111364200-111368800	Active TSS	Brain Anterior Caudate	brain
37	chr13:111364200-111368800	Active TSS	Fetal Kidney	kidney
38	chr13:111364200-111368800	Active TSS	Placenta Amnion	Placenta Amnion
39	chr13:111364200-111368800	Active TSS	Small Intestine	intestine
40	chr13:111364200-111369000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr13:111364200-111369000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr13:111364200-111369000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr13:111364200-111369000	Active TSS	Aorta	Aorta
44	chr13:111364200-111369000	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
45	chr13:111364200-111369000	Active TSS	Placenta	Placenta
46	chr13:111364200-111369000	Active TSS	Pancreas	Pancrea
47	chr13:111364200-111369000	Active TSS	Rectal Mucosa Donor 31	rectum
48	chr13:111364200-111369000	Active TSS	Skeletal Muscle Male	skeletal muscle
49	chr13:111364200-111369000	Active TSS	A549	lung
50	chr13:111364200-111369000	Active TSS	HMEC	breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links