Variant report

Variant	rs2588518
Chromosome Location	chr2:55223282-55223283
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55221662..55224053-chr2:55225919..55227544,2	MCF-7	breast:
2	chr2:55215896..55218354-chr2:55222752..55225132,2	K562	blood:
3	chr2:55221144..55223516-chr2:55232255..55235111,2	K562	blood:
4	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:

Extended variants
information (count: 49 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10174838	0.95[ASN][1000 genomes]
rs10210840	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10496037	0.89[LWK][hapmap]
rs12464070	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12477711	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12713284	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs13387751	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2015919	0.89[ASN][1000 genomes]
rs2044291	0.93[ASN][1000 genomes]
rs2255112	0.97[CHD][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2255393	0.85[JPT][hapmap]
rs2580764	0.81[ASN][1000 genomes]
rs2580765	0.97[CHD][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2580772	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.95[JPT][hapmap];0.80[MEX][hapmap];0.95[ASN][1000 genomes]
rs2580776	0.95[ASN][1000 genomes]
rs2588510	0.82[CHB][hapmap];0.88[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs2588514	0.89[ASN][1000 genomes]
rs2588517	0.86[CHB][hapmap];0.85[CHD][hapmap];0.82[JPT][hapmap];0.80[LWK][hapmap];0.90[ASN][1000 genomes]
rs2588519	0.81[JPT][hapmap];0.84[LWK][hapmap]
rs2588521	0.86[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2860453	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs2902649	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2919129	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2920878	0.85[CEU][hapmap]
rs2920893	0.85[ASN][1000 genomes]
rs2968786	0.88[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs2968787	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968794	0.84[CEU][hapmap]
rs2968795	0.85[CEU][hapmap]
rs2968804	0.82[JPT][hapmap]
rs2972072	0.81[CEU][hapmap]
rs2972075	0.84[CEU][hapmap]
rs2972090	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs2972097	0.92[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs35631428	0.90[ASN][1000 genomes]
rs35826668	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3806570	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4672005	0.93[ASN][1000 genomes]
rs6545466	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs6726158	0.95[ASN][1000 genomes]
rs6755468	0.88[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.80[MEX][hapmap];0.92[ASN][1000 genomes]
rs6760429	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7340476	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7562292	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs7570629	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap]
rs7584430	0.86[ASN][1000 genomes]
rs968998	0.86[CHB][hapmap];0.82[JPT][hapmap];0.84[YRI][hapmap];0.89[ASN][1000 genomes]

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	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
rs2588518	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs2588518	RTN4	cis	Artery Tibial	GTEx
rs2588518	RTN4	cis	Nerve Tibial	GTEx
rs2588518	RTN4	cis	Esophagus Mucosa	GTEx
rs2588518	RTN4	cis	Esophagus Muscularis	GTEx
rs2588518	RTN4	cis	Artery Aorta	GTEx
rs2588518	RTN4	cis	Adipose Subcutaneous	GTEx
rs2588518	RTN4	cis	Whole Blood	GTEx
rs2588518	RTN4	cis	Thyroid	GTEx

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55191800-55234200	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:55196200-55226400	Weak transcription	Thymus	Thymus
3	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
5	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
6	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
7	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
10	chr2:55213800-55226400	Weak transcription	Ovary	ovary
11	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
12	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
15	chr2:55214600-55225600	Weak transcription	NH-A	brain
16	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr2:55214800-55223800	Weak transcription	Gastric	stomach
19	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
22	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:55214800-55225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:55214800-55225200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr2:55214800-55225200	Weak transcription	Fetal Brain Male	brain
26	chr2:55214800-55225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
27	chr2:55214800-55225600	Weak transcription	Brain Germinal Matrix	brain
28	chr2:55214800-55226000	Weak transcription	HUVEC	blood vessel
29	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
30	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
31	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr2:55214800-55227200	Weak transcription	HepG2	liver
33	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
34	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
35	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
36	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
37	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr2:55215000-55225200	Weak transcription	Liver	Liver
39	chr2:55215000-55225800	Weak transcription	Primary B cells from cord blood	blood
40	chr2:55215000-55225800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr2:55215000-55225800	Weak transcription	Hela-S3	cervix
42	chr2:55215200-55225000	Weak transcription	Monocytes-CD14+_RO01746	blood
43	chr2:55215200-55225400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr2:55215200-55227200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr2:55215200-55234200	Weak transcription	Dnd41	blood
46	chr2:55215400-55224400	Weak transcription	Primary hematopoietic stem cells	blood
47	chr2:55215400-55224400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
48	chr2:55216000-55226000	Weak transcription	Right Atrium	heart
49	chr2:55216200-55224800	Weak transcription	K562	blood
50	chr2:55216200-55224800	Weak transcription	NHLF	lung

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