Variant report

Variant	rs2920900
Chromosome Location	chr2:55280083-55280084
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	CHD1	chr2:55271552-55280181	IMR90	lung:	n/a	chr2:55276840-55276850
2	FOS	chr2:55278214-55280128	MCF10A-Er-Src	breast:	n/a	chr2:55278401-55278411 chr2:55278400-55278412 chr2:55278401-55278411 chr2:55278398-55278409 chr2:55279171-55279183 chr2:55278402-55278411 chr2:55278401-55278411 chr2:55278506-55278517 chr2:55278401-55278411
3	RAD21	chr2:55279912-55280141	IMR90	lung:	n/a	n/a
4	BATF	chr2:55279824-55280106	GM12878	blood:	n/a	chr2:55279999-55280007
5	MAFK	chr2:55279857-55280095	IMR90	lung:	n/a	n/a
6	FOS	chr2:55279798-55280132	MCF10A-Er-Src	breast:	n/a	n/a
7	RCOR1	chr2:55279767-55280180	IMR90	lung:	n/a	n/a
8	POLR2A	chr2:55274556-55280140	IMR90	lung:	n/a	n/a
9	RUNX3	chr2:55279786-55280131	GM12878	blood:	n/a	n/a
10	JUN	chr2:55279957-55280704	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55278226..55280278-chr2:55389625..55391199,2	MCF-7	breast:
2	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
3	chr2:55278606..55281085-chr2:55289009..55290511,2	K562	blood:
4	chr2:55279956..55282350-chr2:55389384..55392221,3	K562	blood:
5	chr2:55278300..55281080-chr2:55325086..55327233,3	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000266376	Chromatin interaction
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10174838	0.83[EUR][1000 genomes]
rs10210840	0.83[EUR][1000 genomes]
rs11674808	0.96[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12713284	0.85[EUR][1000 genomes]
rs13011689	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13387751	0.84[EUR][1000 genomes]
rs2044291	0.84[EUR][1000 genomes]
rs2580772	0.82[EUR][1000 genomes]
rs2580776	0.82[EUR][1000 genomes]
rs2860453	0.86[EUR][1000 genomes]
rs2919129	0.82[EUR][1000 genomes]
rs2920878	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920893	0.86[EUR][1000 genomes]
rs2968786	0.86[EUR][1000 genomes]
rs2968790	0.85[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968793	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968794	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2968795	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968822	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2968825	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968827	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2972070	0.84[EUR][1000 genomes]
rs2972071	0.83[ASN][1000 genomes]
rs2972072	0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2972075	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2972097	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs35631428	0.84[EUR][1000 genomes]
rs4672005	0.83[EUR][1000 genomes]
rs6545466	0.85[EUR][1000 genomes]
rs6726158	0.84[EUR][1000 genomes]
rs6755468	0.83[EUR][1000 genomes]
rs6760429	0.85[EUR][1000 genomes]
rs7340476	0.84[EUR][1000 genomes]
rs7562292	0.85[EUR][1000 genomes]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2920900	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2920900	RTN4	cis	Adipose Subcutaneous	GTEx
rs2920900	RTN4	cis	Nerve Tibial	GTEx
rs2920900	RTN4	cis	Artery Tibial	GTEx
rs2920900	RTN4	cis	Whole Blood	GTEx
rs2920900	RTN4	cis	Artery Aorta	GTEx
rs2920900	RTN4	cis	Thyroid	GTEx
rs2920900	RTN4	cis	Esophagus Muscularis	GTEx
rs2920900	RTN4	cis	Esophagus Mucosa	GTEx

Chromatin state (count:70 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55278000-55280200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr2:55278200-55282600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55278200-55288800	Weak transcription	Lung	lung
4	chr2:55278400-55280200	Enhancers	Primary monocytes fromperipheralblood	blood
5	chr2:55278600-55280200	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr2:55278600-55281000	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr2:55278600-55281600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr2:55278600-55282000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
9	chr2:55278800-55280600	Active TSS	K562	blood
10	chr2:55278800-55282200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
11	chr2:55278800-55283200	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:55278800-55283200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:55278800-55288600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:55279000-55280200	Enhancers	Rectal Mucosa Donor 29	rectum
16	chr2:55279000-55280400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr2:55279000-55282000	Enhancers	Primary B cells from peripheral blood	blood
18	chr2:55279000-55282400	Enhancers	Primary T helper cells fromperipheralblood	blood
19	chr2:55279000-55283200	Weak transcription	H1 Cell Line	embryonic stem cell
20	chr2:55279000-55287000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
21	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
22	chr2:55279200-55280400	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr2:55279400-55280200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr2:55279400-55280200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr2:55279400-55280200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr2:55279400-55280200	Enhancers	Hela-S3	cervix
27	chr2:55279400-55281000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr2:55279400-55281000	Weak transcription	Thymus	Thymus
29	chr2:55279400-55282000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:55279400-55282200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr2:55279400-55283000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr2:55279400-55283200	Weak transcription	Osteobl	bone
33	chr2:55279400-55283400	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr2:55279400-55283400	Weak transcription	Brain Hippocampus Middle	brain
35	chr2:55279400-55287600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr2:55279600-55281400	Enhancers	Primary T helper cells PMA-I stimulated	--
37	chr2:55279600-55281400	Weak transcription	Fetal Kidney	kidney
38	chr2:55279600-55283000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr2:55279600-55283200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
40	chr2:55279800-55280200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr2:55279800-55280200	Enhancers	NH-A	brain
42	chr2:55279800-55280400	Weak transcription	Fetal Thymus	thymus
43	chr2:55279800-55280400	Enhancers	HUVEC	blood vessel
44	chr2:55279800-55280800	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr2:55279800-55280800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr2:55279800-55280800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr2:55279800-55281400	Enhancers	Primary T cells from cord blood	blood
48	chr2:55279800-55282000	Enhancers	Primary T helper naive cells from peripheral blood	blood
49	chr2:55279800-55282000	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr2:55279800-55282600	Enhancers	Primary B cells from cord blood	blood

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