Variant report

Variant	rs2255393
Chromosome Location	chr2:55197882-55197883
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RTN4-1	chr2:55196736-55198803	ENSG00000248316
2	lnc-EML6-2	chr2:55197791-55198009	NONHSAT070751

Extended variants
information (count: 50 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10210840	0.91[JPT][hapmap]
rs12713284	0.91[JPT][hapmap]
rs13031431	0.85[CHB][hapmap]
rs13387751	0.86[JPT][hapmap]
rs17046579	0.85[CHB][hapmap]
rs17046586	0.85[CHB][hapmap]
rs17046589	0.85[CHB][hapmap]
rs1822617	0.81[CHB][hapmap]
rs2255026	0.85[CHB][hapmap]
rs2255112	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2580765	0.90[JPT][hapmap];0.84[ASN][1000 genomes]
rs2580768	0.85[CHB][hapmap]
rs2580769	0.85[CHB][hapmap]
rs2580770	0.85[CHB][hapmap]
rs2580771	0.85[CHB][hapmap]
rs2580772	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2588510	0.90[JPT][hapmap];0.82[ASN][1000 genomes]
rs2588513	0.85[CHB][hapmap]
rs2588515	0.85[CHB][hapmap]
rs2588516	0.85[CHB][hapmap]
rs2588518	0.85[JPT][hapmap]
rs2588519	0.85[CHB][hapmap];0.86[JPT][hapmap];0.90[ASN][1000 genomes]
rs2588521	0.91[JPT][hapmap];0.84[ASN][1000 genomes]
rs2588522	0.85[CHB][hapmap]
rs2860453	0.91[JPT][hapmap]
rs2919126	0.83[CHB][hapmap]
rs2919129	0.86[JPT][hapmap]
rs2920859	0.85[CHB][hapmap]
rs2920892	0.85[CHB][hapmap]
rs2968786	0.91[JPT][hapmap]
rs2968787	0.90[JPT][hapmap]
rs2968788	0.85[CHB][hapmap]
rs2968804	0.80[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2972092	0.85[CHB][hapmap]
rs2972097	0.91[JPT][hapmap]
rs4672003	0.85[CHB][hapmap]
rs6545464	0.85[CHB][hapmap]
rs6545465	0.80[CHB][hapmap]
rs6545466	0.91[JPT][hapmap]
rs6734314	0.85[CHB][hapmap]
rs6739210	0.81[CHB][hapmap]
rs6755468	0.86[JPT][hapmap]
rs6760429	0.91[JPT][hapmap]
rs7340476	0.86[JPT][hapmap]
rs7562292	0.91[JPT][hapmap]
rs7570629	0.91[JPT][hapmap]
rs7584430	0.84[ASN][1000 genomes]
rs887	0.84[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv834069	chr2:55096597-55251680	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
2	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2255393	RTN4	cis	Whole Blood	GTEx
rs2255393	RTN4	cis	Esophagus Muscularis	GTEx
rs2255393	RTN4	cis	Esophagus Mucosa	GTEx
rs2255393	RTN4	cis	Thyroid	GTEx
rs2255393	RTN4	cis	Nerve Tibial	GTEx
rs2255393	RTN4	cis	Artery Tibial	GTEx
rs2255393	RTN4	cis	Adipose Subcutaneous	GTEx
rs2255393	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55173200-55203400	Weak transcription	Gastric	stomach
2	chr2:55181600-55203400	Weak transcription	Ovary	ovary
3	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
4	chr2:55184800-55214800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55190000-55198400	Weak transcription	Colonic Mucosa	Colon
6	chr2:55190000-55203400	Weak transcription	Small Intestine	intestine
7	chr2:55190600-55198000	Genic enhancers	Fetal Muscle Leg	muscle
8	chr2:55191200-55198200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:55191200-55199200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:55191800-55203600	Weak transcription	Fetal Lung	lung
11	chr2:55191800-55211600	Weak transcription	Placenta Amnion	Placenta Amnion
12	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr2:55192200-55198600	Strong transcription	Fetal Stomach	stomach
14	chr2:55192600-55198600	Strong transcription	Fetal Intestine Small	intestine
15	chr2:55193400-55199000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
16	chr2:55193400-55201800	Strong transcription	Muscle Satellite Cultured Cells	--
17	chr2:55193400-55214800	Strong transcription	HepG2	liver
18	chr2:55193600-55200800	Strong transcription	A549	lung
19	chr2:55193600-55201800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
20	chr2:55193600-55214600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr2:55193800-55198200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:55193800-55198600	Genic enhancers	Lung	lung
23	chr2:55193800-55202400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr2:55193800-55211800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr2:55194000-55198600	Strong transcription	Brain Germinal Matrix	brain
26	chr2:55194000-55199000	Strong transcription	Stomach Smooth Muscle	stomach
27	chr2:55194000-55211800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr2:55194200-55198600	Weak transcription	Primary T helper cells PMA-I stimulated	--
29	chr2:55194200-55204400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
30	chr2:55194400-55198200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr2:55194400-55200200	Strong transcription	Primary neutrophils fromperipheralblood	blood
32	chr2:55194400-55200200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
33	chr2:55194400-55201400	Strong transcription	Primary B cells from cord blood	blood
34	chr2:55194600-55202200	Strong transcription	NHDF-Ad	bronchial
35	chr2:55194600-55204400	Strong transcription	Primary T cells from cord blood	blood
36	chr2:55194800-55201200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr2:55194800-55202400	Strong transcription	NHLF	lung
38	chr2:55195000-55198000	Enhancers	Left Ventricle	heart
39	chr2:55195000-55199600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr2:55195000-55203200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
41	chr2:55195000-55215200	Strong transcription	Dnd41	blood
42	chr2:55195200-55199200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
43	chr2:55195200-55201200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr2:55195200-55201600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr2:55195200-55202000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr2:55195200-55202600	Strong transcription	Osteobl	bone
47	chr2:55195200-55205600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
48	chr2:55195200-55205800	Strong transcription	HMEC	breast
49	chr2:55195400-55198600	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr2:55195400-55199400	Strong transcription	Fetal Intestine Large	intestine

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