Variant report

Variant	rs2920863
Chromosome Location	chr2:55315139-55315140
allele	C/G
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	chr2:55311726..55313252-chr2:55313684..55315379,2	K562	blood:
3	chr2:55300544..55302491-chr2:55314911..55316564,2	K562	blood:
4	chr2:55313997..55316994-chr2:55461231..55462844,2	K562	blood:
5	chr2:55277836..55279728-chr2:55313964..55316621,2	K562	blood:
6	chr2:55306855..55308642-chr2:55313983..55316213,2	K562	blood:
7	chr2:55306577..55308531-chr2:55314255..55316855,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10179594	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs10196667	0.82[CEU][hapmap]
rs10205017	0.80[EUR][1000 genomes]
rs10746530	0.82[CEU][hapmap]
rs11125551	0.82[CEU][hapmap]
rs12989576	0.82[CEU][hapmap];0.83[EUR][1000 genomes]
rs13002841	0.82[CEU][hapmap];0.80[EUR][1000 genomes]
rs13023202	0.82[EUR][1000 genomes]
rs2580763	0.80[EUR][1000 genomes]
rs2580766	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2588520	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2919125	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920839	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2920861	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920881	1.00[CHB][hapmap]
rs2920883	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920884	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920889	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920890	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2920898	0.85[CHB][hapmap]
rs2968789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2968812	1.00[CHB][hapmap]
rs2968813	1.00[CHB][hapmap]
rs2968814	1.00[CHB][hapmap]
rs2968823	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2968824	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2968826	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2968829	1.00[CHB][hapmap]
rs2968831	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2972065	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972066	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2972069	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2972076	0.90[EUR][1000 genomes]
rs3099068	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4672018	0.90[JPT][hapmap]
rs6545462	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs7559248	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2920863	RTN4	cis	Thyroid	GTEx

Chromatin state (count:30 , 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	chr2:55309200-55315200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr2:55312000-55316800	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr2:55312000-55317400	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr2:55312000-55321200	Weak transcription	Lung	lung
6	chr2:55314200-55315400	Enhancers	Brain Inferior Temporal Lobe	brain
7	chr2:55314200-55316000	Enhancers	Fetal Lung	lung
8	chr2:55314400-55315400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr2:55314400-55315400	Enhancers	A549	lung
10	chr2:55314600-55315400	Enhancers	Muscle Satellite Cultured Cells	--
11	chr2:55314600-55315400	Enhancers	Brain Angular Gyrus	brain
12	chr2:55314600-55315400	Enhancers	Brain Cingulate Gyrus	brain
13	chr2:55314600-55315400	Enhancers	Brain Hippocampus Middle	brain
14	chr2:55314600-55315600	Enhancers	HUVEC	blood vessel
15	chr2:55314600-55315600	Enhancers	NHLF	lung
16	chr2:55314600-55316000	Enhancers	Brain Substantia Nigra	brain
17	chr2:55314600-55318400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr2:55314800-55315400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr2:55314800-55315400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
20	chr2:55314800-55315800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
21	chr2:55314800-55316000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:55314800-55316000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:55314800-55316000	Enhancers	NHDF-Ad	bronchial
24	chr2:55314800-55316000	Enhancers	Osteobl	bone
25	chr2:55314800-55317000	Enhancers	Fetal Stomach	stomach
26	chr2:55314800-55317200	Enhancers	Fetal Muscle Leg	muscle
27	chr2:55315000-55315200	Enhancers	Fetal Heart	heart
28	chr2:55315000-55315200	Flanking Active TSS	K562	blood
29	chr2:55315000-55318000	Weak transcription	Hela-S3	cervix
30	chr2:55315000-55319400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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