Variant report

Variant	rs2920862
Chromosome Location	chr2:55316938-55316939
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55309144..55311661-chr2:55314427..55318457,3	K562	blood:
2	chr2:55315606..55317347-chr2:55338436..55340303,2	K562	blood:
3	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:
4	chr2:55315563..55318504-chr2:55346291..55347986,2	K562	blood:
5	chr2:55315251..55317504-chr2:55320953..55322890,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11674808	0.85[ASN][1000 genomes]
rs13011689	0.86[ASN][1000 genomes]
rs2920878	0.87[CHB][hapmap];0.96[JPT][hapmap];0.89[ASN][1000 genomes]
rs2968790	0.81[ASN][1000 genomes]
rs2968793	0.86[ASN][1000 genomes]
rs2968794	0.91[CHB][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2968795	0.87[CHB][hapmap];0.96[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968798	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2968822	0.96[ASN][1000 genomes]
rs2968825	0.94[ASN][1000 genomes]
rs2968827	0.89[ASN][1000 genomes]
rs2972070	0.90[ASN][1000 genomes]
rs2972071	0.90[ASN][1000 genomes]
rs2972072	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2972075	0.91[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2920862	RTN4	cis	Whole Blood	GTEx
rs2920862	RTN4	cis	Artery Aorta	GTEx
rs2920862	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55299200-55318000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:55312000-55317400	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr2:55312000-55321200	Weak transcription	Lung	lung
4	chr2:55314600-55318400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr2:55314800-55317000	Enhancers	Fetal Stomach	stomach
6	chr2:55314800-55317200	Enhancers	Fetal Muscle Leg	muscle
7	chr2:55315000-55318000	Weak transcription	Hela-S3	cervix
8	chr2:55315000-55319400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr2:55315400-55317200	Enhancers	Fetal Heart	heart
10	chr2:55315400-55317800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr2:55315400-55319200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr2:55315400-55319800	Weak transcription	A549	lung
13	chr2:55315400-55320200	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr2:55315400-55320200	Weak transcription	Brain Angular Gyrus	brain
15	chr2:55315400-55320200	Weak transcription	Brain Cingulate Gyrus	brain
16	chr2:55315400-55320600	Weak transcription	Brain Hippocampus Middle	brain
17	chr2:55315400-55320800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr2:55315400-55323600	Weak transcription	HSMMtube	muscle
19	chr2:55315600-55317800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
20	chr2:55315600-55317800	Weak transcription	NHLF	lung
21	chr2:55315600-55319000	Enhancers	K562	blood
22	chr2:55315600-55319600	Weak transcription	HUVEC	blood vessel
23	chr2:55315800-55317600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:55316000-55317800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr2:55316000-55317800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr2:55316000-55318000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:55316000-55320000	Weak transcription	Osteobl	bone
28	chr2:55316000-55320600	Weak transcription	Brain Substantia Nigra	brain
29	chr2:55316000-55322800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55316000-55323800	Weak transcription	NHDF-Ad	bronchial
31	chr2:55316200-55317000	Enhancers	Fetal Muscle Trunk	muscle
32	chr2:55316400-55317400	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr2:55316800-55318200	Enhancers	HSMM	muscle
34	chr2:55316800-55327200	Enhancers	Primary neutrophils fromperipheralblood	blood

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