Variant report

Variant	rs6545466
Chromosome Location	chr2:55228392-55228393
allele	C/T
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..55228646-chr2:55241390..55244484,3	K562	blood:
3	chr2:55226114..55228933-chr2:55231694..55233416,2	MCF-7	breast:
4	chr2:55228095..55231014-chr2:55462298..55463930,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000200086	Chromatin interaction

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

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

rs_ID	r²[population]
rs10174838	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10210840	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11674808	0.85[EUR][1000 genomes]
rs12464070	0.91[ASN][1000 genomes]
rs12477711	0.94[ASN][1000 genomes]
rs12713284	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]
rs13011689	0.87[EUR][1000 genomes]
rs13387751	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2015919	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2044291	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2255112	1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2255393	0.91[JPT][hapmap]
rs2580764	0.82[ASN][1000 genomes]
rs2580765	1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2580772	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2580773	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2580776	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588510	0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2588514	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2588517	0.91[CHB][hapmap];0.88[ASN][1000 genomes]
rs2588518	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs2588519	0.86[JPT][hapmap]
rs2588521	0.91[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2860453	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902649	0.94[ASN][1000 genomes]
rs2919129	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920878	0.93[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920893	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2920900	0.85[EUR][1000 genomes]
rs2968786	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968787	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs2968790	0.86[EUR][1000 genomes]
rs2968793	0.87[EUR][1000 genomes]
rs2968794	0.92[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968795	0.93[CEU][hapmap];0.87[EUR][1000 genomes]
rs2968804	0.87[JPT][hapmap]
rs2972072	0.88[CEU][hapmap];0.85[EUR][1000 genomes]
rs2972075	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs2972090	0.87[CHB][hapmap];0.83[JPT][hapmap];0.81[ASN][1000 genomes]
rs2972097	1.00[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35631428	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35826668	0.99[ASN][1000 genomes]
rs3806570	0.97[ASN][1000 genomes]
rs4672005	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6726158	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6755468	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6760429	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7340476	0.96[CEU][hapmap];0.91[CHB][hapmap];0.96[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7562292	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7570629	0.93[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes]
rs7584430	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs968998	0.91[CHB][hapmap];0.88[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
rs6545466	RTN4	cis	Artery Tibial	GTEx
rs6545466	RTN4	cis	Nerve Tibial	GTEx
rs6545466	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs6545466	RTN4	cis	Esophagus Mucosa	GTEx
rs6545466	RTN4	cis	Adipose Subcutaneous	GTEx
rs6545466	RTN4	cis	Thyroid	GTEx
rs6545466	RTN4	cis	Artery Aorta	GTEx
rs6545466	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	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
8	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
9	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
10	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr2:55215200-55234200	Weak transcription	Dnd41	blood
13	chr2:55219400-55228800	Weak transcription	Aorta	Aorta
14	chr2:55219400-55233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:55220400-55236800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr2:55222800-55228600	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr2:55222800-55229000	Enhancers	Brain Anterior Caudate	brain
18	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:55224400-55228800	Enhancers	Adipose Nuclei	Adipose
20	chr2:55224600-55229400	Enhancers	Breast Myoepithelial Primary Cells	Breast
21	chr2:55224800-55229000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr2:55224800-55229000	Enhancers	Fetal Heart	heart
23	chr2:55224800-55230200	Enhancers	Muscle Satellite Cultured Cells	--
24	chr2:55224800-55231000	Weak transcription	Small Intestine	intestine
25	chr2:55224800-55236800	Enhancers	A549	lung
26	chr2:55225000-55228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr2:55225000-55228400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:55225000-55228400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:55225200-55234600	Enhancers	Liver	Liver
30	chr2:55225600-55228800	Enhancers	HUES64 Cell Line	embryonic stem cell
31	chr2:55225800-55228800	Enhancers	Primary T helper naive cells from peripheral blood	blood
32	chr2:55225800-55229000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
33	chr2:55226000-55228400	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
34	chr2:55226000-55228600	Enhancers	Brain Inferior Temporal Lobe	brain
35	chr2:55226000-55228800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr2:55226000-55230800	Enhancers	HUVEC	blood vessel
37	chr2:55226400-55229000	Enhancers	Cortex derived primary cultured neurospheres	brain
38	chr2:55226400-55230000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr2:55226600-55228400	Weak transcription	Fetal Kidney	kidney
40	chr2:55226600-55228600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr2:55226600-55229000	Enhancers	Duodenum Smooth Muscle	Duodenum
42	chr2:55226600-55229000	Weak transcription	Ovary	ovary
43	chr2:55226600-55230200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr2:55226600-55230400	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr2:55226600-55233800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr2:55226600-55237200	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:55226800-55229200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr2:55226800-55229200	Weak transcription	Fetal Muscle Leg	muscle
49	chr2:55226800-55229800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
50	chr2:55226800-55229800	Enhancers	Osteobl	bone

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