Variant report

Variant	rs12713284
Chromosome Location	chr2:55228861-55228862
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55228082..55231303-chr2:55231498..55236378,7	K562	blood:
2	chr2:55226114..55228933-chr2:55231694..55233416,2	MCF-7	breast:
3	chr2:55228095..55231014-chr2:55462298..55463930,2	MCF-7	breast:

Extended variants
information (count: 54 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10174838	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11674808	0.85[EUR][1000 genomes]
rs12464070	0.87[ASN][1000 genomes]
rs12477711	0.90[ASN][1000 genomes]
rs13011689	0.87[EUR][1000 genomes]
rs13387751	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2015919	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2044291	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2255112	0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2255393	0.91[JPT][hapmap]
rs2580764	0.83[ASN][1000 genomes]
rs2580765	0.86[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2580772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2580773	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2580776	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2588510	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2588514	0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2588517	1.00[CHB][hapmap];0.89[ASN][1000 genomes]
rs2588518	0.88[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[ASN][1000 genomes]
rs2588519	0.86[JPT][hapmap]
rs2588521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2860453	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2902649	0.90[ASN][1000 genomes]
rs2919129	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920893	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920900	0.85[EUR][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968787	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968790	0.86[EUR][1000 genomes]
rs2968793	0.87[EUR][1000 genomes]
rs2968794	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.87[EUR][1000 genomes]
rs2968804	0.87[JPT][hapmap]
rs2972072	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2972075	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2972090	0.95[CHB][hapmap];0.83[JPT][hapmap];0.83[ASN][1000 genomes]
rs2972097	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35631428	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35826668	0.95[ASN][1000 genomes]
rs3806570	0.92[ASN][1000 genomes]
rs4672005	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6545466	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6726158	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6755468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6760429	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7340476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7562292	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570629	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs7584430	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs968998	1.00[CHB][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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs12713284	RTN4	cis	Artery Aorta	GTEx
rs12713284	RTN4	cis	Thyroid	GTEx
rs12713284	RTN4	cis	Artery Tibial	GTEx
rs12713284	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs12713284	RTN4	cis	Nerve Tibial	GTEx
rs12713284	RTN4	cis	Esophagus Mucosa	GTEx
rs12713284	RTN4	cis	Adipose Subcutaneous	GTEx
rs12713284	RTN4	cis	Whole Blood	GTEx

Chromatin state (count:108 , 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	chr2:55198200-55237200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
4	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
6	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
7	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:55215200-55234200	Weak transcription	Dnd41	blood
12	chr2:55219400-55233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
13	chr2:55220400-55236800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
14	chr2:55222800-55229000	Enhancers	Brain Anterior Caudate	brain
15	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr2:55224600-55229400	Enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr2:55224800-55229000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr2:55224800-55229000	Enhancers	Fetal Heart	heart
19	chr2:55224800-55230200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr2:55224800-55231000	Weak transcription	Small Intestine	intestine
21	chr2:55224800-55236800	Enhancers	A549	lung
22	chr2:55225200-55234600	Enhancers	Liver	Liver
23	chr2:55225800-55229000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr2:55226000-55230800	Enhancers	HUVEC	blood vessel
25	chr2:55226400-55229000	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr2:55226400-55230000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55226600-55229000	Enhancers	Duodenum Smooth Muscle	Duodenum
28	chr2:55226600-55229000	Weak transcription	Ovary	ovary
29	chr2:55226600-55230200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55226600-55230400	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr2:55226600-55233800	Weak transcription	Primary hematopoietic stem cells	blood
32	chr2:55226600-55237200	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr2:55226800-55229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr2:55226800-55229200	Weak transcription	Fetal Muscle Leg	muscle
35	chr2:55226800-55229800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr2:55226800-55229800	Enhancers	Osteobl	bone
37	chr2:55226800-55231000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
38	chr2:55226800-55235200	Enhancers	Colon Smooth Muscle	Colon
39	chr2:55226800-55236600	Weak transcription	Right Atrium	heart
40	chr2:55226800-55237000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr2:55227000-55229000	Enhancers	iPS-15b Cell Line	embryonic stem cell
42	chr2:55227000-55230600	Weak transcription	Fetal Intestine Small	intestine
43	chr2:55227000-55232200	Enhancers	NHEK	skin
44	chr2:55227000-55236600	Weak transcription	Brain Germinal Matrix	brain
45	chr2:55227200-55230200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
46	chr2:55227200-55232600	Enhancers	Brain Angular Gyrus	brain
47	chr2:55227200-55233400	Weak transcription	Fetal Thymus	thymus
48	chr2:55227200-55236800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr2:55227400-55232200	Weak transcription	Fetal Lung	lung
50	chr2:55227400-55236800	Weak transcription	Fetal Brain Male	brain

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