Variant report

Variant	rs4771707
Chromosome Location	chr13:111363635-111363636
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:3)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:3 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr13:111363612-111368813	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr13:111363572-111363857	K562	blood:	n/a	n/a
3	POLR2A	chr13:111363549-111368807	HepG2	liver:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr13:111362764..111370771-chr13:111560775..111570046,21	K562	blood:
2	chr13:111328800..111332502-chr13:111363272..111367932,6	K562	blood:
3	chr13:111362818..111369538-chr13:111519409..111528258,26	K562	blood:
4	chr13:111294769..111302902-chr13:111363368..111369699,14	K562	blood:
5	chr13:111362370..111368494-chr13:111564438..111569891,17	K562	blood:
6	chr13:111211605..111215710-chr13:111363534..111368936,10	MCF-7	breast:
7	chr13:111265756..111270693-chr13:111363417..111370660,10	K562	blood:
8	chr13:111363080..111368100-chr13:111564424..111568464,9	MCF-7	breast:
9	chr13:111335461..111337308-chr13:111363462..111365716,2	MCF-7	breast:
10	chr13:111363576..111369085-chr13:111458761..111470393,19	MCF-7	breast:

No data

Variant related genes	Relation type
ING1	TF binding region
CARS2	TF binding region
ENSG00000139832	Chromatin interaction
ENSG00000255874	Chromatin interaction
ENSG00000259831	Chromatin interaction
ENSG00000134905	Chromatin interaction
ENSG00000213995	Chromatin interaction
ENSG00000088448	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 2 )

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	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12875067	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441042	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1441043	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2083568	0.83[AMR][1000 genomes]
rs2119479	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2165418	0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2289461	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3809344	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3818496	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4773240	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773241	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4773244	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61971615	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6492302	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6492303	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6492304	0.89[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6492305	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6492306	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6492308	0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7318291	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7319459	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7330080	0.91[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]
rs754599	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7984468	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7985098	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7986286	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7991766	0.86[EUR][1000 genomes]
rs9301476	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9515273	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9515274	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9521905	0.89[EUR][1000 genomes]
rs9521909	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9521910	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9521913	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9521914	0.85[EUR][1000 genomes]
rs9521915	0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9555724	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9555726	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9559863	0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9588247	0.88[EUR][1000 genomes];0.91[ASN][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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4771707	CARS2	cis	Nerve Tibial	GTEx
rs4771707	CARS2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:111359200-111363800	Weak transcription	HUES48 Cell Line	embryonic stem cell
2	chr13:111359200-111363800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr13:111359200-111363800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr13:111359200-111363800	Weak transcription	Stomach Mucosa	stomach
5	chr13:111359200-111363800	Weak transcription	HSMMtube	muscle
6	chr13:111359200-111364000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr13:111359400-111363800	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr13:111359400-111363800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:111359400-111363800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
10	chr13:111359400-111363800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr13:111359400-111363800	Weak transcription	Brain Anterior Caudate	brain
12	chr13:111359400-111363800	Weak transcription	HMEC	breast
13	chr13:111359400-111363800	Weak transcription	HSMM	muscle
14	chr13:111359400-111363800	Weak transcription	NHEK	skin
15	chr13:111359400-111363800	Weak transcription	Osteobl	bone
16	chr13:111359400-111364000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr13:111359400-111364000	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr13:111359600-111363800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:111359600-111363800	Weak transcription	Primary T cells from cord blood	blood
20	chr13:111359600-111363800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr13:111359600-111363800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
22	chr13:111359600-111363800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr13:111359600-111363800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr13:111359600-111363800	Weak transcription	Brain Angular Gyrus	brain
25	chr13:111359600-111363800	Weak transcription	Brain Cingulate Gyrus	brain
26	chr13:111359600-111363800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr13:111359600-111363800	Weak transcription	Brain Substantia Nigra	brain
28	chr13:111359600-111363800	Weak transcription	Colon Smooth Muscle	Colon
29	chr13:111359600-111363800	Weak transcription	Duodenum Mucosa	Duodenum
30	chr13:111359600-111364000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr13:111359600-111364000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr13:111359600-111364000	Weak transcription	Esophagus	oesophagus
33	chr13:111359800-111363800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr13:111359800-111364000	Weak transcription	Gastric	stomach
35	chr13:111361000-111363800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr13:111361600-111363800	Enhancers	Primary monocytes fromperipheralblood	blood
37	chr13:111362200-111363800	Enhancers	Primary neutrophils fromperipheralblood	blood
38	chr13:111362200-111363800	Enhancers	Primary B cells from cord blood	blood
39	chr13:111363000-111363800	Enhancers	Primary hematopoietic stem cells	blood
40	chr13:111363000-111363800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr13:111363000-111363800	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr13:111363400-111363800	Enhancers	Primary T helper cells PMA-I stimulated	--
43	chr13:111363400-111363800	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr13:111363400-111363800	Enhancers	Liver	Liver
45	chr13:111363400-111363800	Enhancers	Fetal Heart	heart
46	chr13:111363400-111363800	Enhancers	Fetal Lung	lung
47	chr13:111363400-111363800	Enhancers	Fetal Thymus	thymus
48	chr13:111363400-111363800	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr13:111363400-111363800	Enhancers	A549	lung
50	chr13:111363400-111363800	Enhancers	GM12878-XiMat	blood

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