Variant report

Variant	rs1012603
Chromosome Location	chr2:55274531-55274532
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:17)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:17 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MXI1	chr2:55273915-55275492	IMR90	lung:	n/a	n/a
2	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
3	CEBPB	chr2:55273676-55274742	A549	lung:	n/a	n/a
4	CEBPB	chr2:55273863-55274555	IMR90	lung:	n/a	n/a
5	CEBPB	chr2:55274254-55274618	K562	blood:	n/a	n/a
6	TEAD4	chr2:55273707-55274611	HepG2	liver:	n/a	n/a
7	MYC	chr2:55274263-55274688	K562	blood:	n/a	n/a
8	CEBPB	chr2:55274025-55274612	H1-hESC	embryonic stem cell:	n/a	n/a
9	CTCF	chr2:55274353-55279779	A549	lung:	n/a	n/a
10	JUND	chr2:55274260-55274970	K562	blood:	n/a	n/a
11	POLR2A	chr2:55274490-55275446	U87	brain:	n/a	n/a
12	POLR2A	chr2:55274496-55275508	U87	brain:	n/a	n/a
13	CEBPB	chr2:55274250-55275293	K562	blood:	n/a	chr2:55275098-55275109
14	CEBPB	chr2:55274255-55274672	A549	lung:	n/a	n/a
15	RAD21	chr2:55274531-55278955	SK-N-SH	brain:	n/a	chr2:55277716-55277726
16	ZNF384	chr2:55274261-55274682	K562	blood:	n/a	n/a
17	ATF3	chr2:55274252-55274646	K562	blood:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55273795..55276620-chr2:55843969..55846667,2	K562	blood:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
4	chr2:54196421..54198197-chr2:55274517..55277399,2	MCF-7	breast:
5	chr2:55273237..55279836-chr2:55336432..55344363,17	K562	blood:
6	chr2:55274277..55275806-chr2:55323435..55326407,2	K562	blood:

No data

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000272606	Chromatin interaction
ENSG00000200086	Chromatin interaction
ENSG00000266376	Chromatin interaction
ENSG00000170634	Chromatin interaction
ENSG00000068878	Chromatin interaction
ENSG00000138041	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10496040	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11696046	1.00[YRI][hapmap]
rs13033042	1.00[YRI][hapmap]
rs17046514	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.81[EUR][1000 genomes]
rs17046518	0.85[AMR][1000 genomes]
rs17046583	0.82[CEU][hapmap];0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs17046643	1.00[CEU][hapmap];1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17046658	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2028728	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs2241958	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2255026	0.83[AFR][1000 genomes]
rs2580771	0.83[AFR][1000 genomes]
rs2588515	0.83[AFR][1000 genomes]
rs2588516	0.83[AFR][1000 genomes]
rs2588522	0.83[AFR][1000 genomes]
rs2919126	0.83[AFR][1000 genomes]
rs34378852	0.83[AFR][1000 genomes]
rs4671993	1.00[CEU][hapmap]
rs4672006	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4672009	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4672011	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs57737203	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60553807	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs60989687	0.81[EUR][1000 genomes]
rs6545464	0.83[AFR][1000 genomes]
rs6734314	0.83[AFR][1000 genomes]
rs6739210	0.83[AFR][1000 genomes]
rs73936818	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73936829	0.84[EUR][1000 genomes]
rs7595134	1.00[YRI][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1012603	RTN4	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:120 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55259400-55275200	Weak transcription	Esophagus	oesophagus
2	chr2:55268000-55274800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
3	chr2:55271400-55275000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:55271400-55278200	Active TSS	HSMMtube	muscle
5	chr2:55271600-55274600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
6	chr2:55271600-55274800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:55271600-55275000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr2:55271600-55275000	Weak transcription	Lung	lung
9	chr2:55271600-55275200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:55271600-55275200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr2:55272000-55274600	Enhancers	Rectal Smooth Muscle	rectum
12	chr2:55272000-55274800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr2:55272000-55275000	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:55272200-55274600	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr2:55272200-55274600	Enhancers	Cortex derived primary cultured neurospheres	brain
16	chr2:55272200-55274600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr2:55272200-55274600	Enhancers	Fetal Lung	lung
18	chr2:55272200-55274800	Enhancers	Fetal Intestine Large	intestine
19	chr2:55272400-55274600	Genic enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:55272400-55275000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr2:55272400-55275000	Flanking Active TSS	HUVEC	blood vessel
22	chr2:55272400-55279600	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:55272600-55274600	Enhancers	Colon Smooth Muscle	Colon
24	chr2:55272600-55274600	Enhancers	Fetal Muscle Leg	muscle
25	chr2:55272600-55274600	Enhancers	Ovary	ovary
26	chr2:55272600-55274600	Enhancers	Sigmoid Colon	Sigmoid Colon
27	chr2:55272600-55274600	Flanking Active TSS	Osteobl	bone
28	chr2:55272600-55274800	Enhancers	Fetal Intestine Small	intestine
29	chr2:55272600-55275200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
30	chr2:55272600-55275400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr2:55272800-55274600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
32	chr2:55272800-55274600	Enhancers	Thymus	Thymus
33	chr2:55272800-55274800	Enhancers	Duodenum Mucosa	Duodenum
34	chr2:55272800-55275000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
35	chr2:55272800-55275600	Transcr. at gene 5' and 3'	HSMM	muscle
36	chr2:55273000-55274600	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55273000-55274600	Enhancers	Primary hematopoietic stem cells	blood
38	chr2:55273000-55274800	Flanking Active TSS	HUES64 Cell Line	embryonic stem cell
39	chr2:55273000-55274800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
40	chr2:55273000-55275000	Enhancers	Primary T cells from cord blood	blood
41	chr2:55273000-55275000	Enhancers	Rectal Mucosa Donor 31	rectum
42	chr2:55273000-55275600	Transcr. at gene 5' and 3'	Dnd41	blood
43	chr2:55273000-55276200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr2:55273000-55276800	Active TSS	ES-WA7 Cell Line	embryonic stem cell
45	chr2:55273200-55275000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr2:55273200-55275200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:55273200-55275200	Weak transcription	Gastric	stomach
48	chr2:55273200-55278400	Active TSS	Rectal Mucosa Donor 29	rectum
49	chr2:55273200-55278400	Active TSS	GM12878-XiMat	blood
50	chr2:55273400-55274600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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