Variant report

Variant	rs7340476
Chromosome Location	chr2:55227346-55227347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55224682..55227904-chr2:55233478..55236485,4	MCF-7	breast:
2	chr2:55226114..55228278-chr2:55241390..55244411,3	K562	blood:
3	chr2:55224031..55227614-chr2:55234894..55236977,3	K562	blood:
4	chr2:55226114..55228646-chr2:55241390..55244484,3	K562	blood:
5	chr2:55221662..55224053-chr2:55225919..55227544,2	MCF-7	breast:
6	chr2:55226114..55228933-chr2:55231694..55233416,2	MCF-7	breast:
7	chr2:55225943..55228351-chr2:55458168..55460994,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143947	Chromatin interaction
ENSG00000162994	Chromatin interaction
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	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10210840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11674808	0.86[EUR][1000 genomes]
rs12464070	0.88[ASN][1000 genomes]
rs12477711	0.91[ASN][1000 genomes]
rs12713284	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]
rs13011689	0.86[EUR][1000 genomes]
rs13387751	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2015919	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2044291	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2255112	0.82[CHB][hapmap];0.95[JPT][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2255393	0.86[JPT][hapmap]
rs2580764	0.85[ASN][1000 genomes]
rs2580765	0.86[CHB][hapmap];0.95[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2580772	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2580773	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2580776	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588510	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588514	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588517	1.00[CHB][hapmap];0.82[JPT][hapmap];0.92[ASN][1000 genomes]
rs2588518	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2588519	0.82[JPT][hapmap]
rs2588521	1.00[CHB][hapmap];0.96[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2860453	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2902649	0.91[ASN][1000 genomes]
rs2919129	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2920893	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920900	0.84[EUR][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2968787	0.85[CEU][hapmap];0.86[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968790	0.84[EUR][1000 genomes]
rs2968793	0.85[EUR][1000 genomes]
rs2968794	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.86[EUR][1000 genomes]
rs2968804	0.83[JPT][hapmap]
rs2972072	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2972075	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2972090	0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs2972097	0.96[CEU][hapmap];0.87[CHB][hapmap];0.96[JPT][hapmap];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35631428	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35826668	0.95[ASN][1000 genomes]
rs3806570	0.94[ASN][1000 genomes]
rs4672005	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6545466	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]
rs6726158	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6755468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6760429	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	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7570629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.82[AMR][1000 genomes]
rs7584430	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs968998	1.00[CHB][hapmap];0.91[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
rs7340476	RTN4	cis	Esophagus Mucosa	GTEx
rs7340476	RTN4	cis	Artery Aorta	GTEx
rs7340476	RTN4	cis	Nerve Tibial	GTEx
rs7340476	RTN4	cis	Whole Blood	GTEx
rs7340476	RTN4	cis	Thyroid	GTEx
rs7340476	RTN4	cis	Artery Tibial	GTEx
rs7340476	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs7340476	RTN4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:111 , 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	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
8	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
9	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr2:55215200-55234200	Weak transcription	Dnd41	blood
14	chr2:55219400-55228800	Weak transcription	Aorta	Aorta
15	chr2:55219400-55233400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr2:55220400-55236800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
17	chr2:55222800-55227800	Enhancers	Brain Substantia Nigra	brain
18	chr2:55222800-55228000	Enhancers	Primary T helper cells PMA-I stimulated	--
19	chr2:55222800-55228600	Enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr2:55222800-55229000	Enhancers	Brain Anterior Caudate	brain
21	chr2:55223000-55237200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr2:55223200-55227400	Weak transcription	Primary B cells from peripheral blood	blood
23	chr2:55224400-55227800	Enhancers	Brain Cingulate Gyrus	brain
24	chr2:55224400-55228000	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr2:55224400-55228800	Enhancers	Adipose Nuclei	Adipose
26	chr2:55224600-55227600	Enhancers	Primary T cells from cord blood	blood
27	chr2:55224600-55227600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
28	chr2:55224600-55228000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr2:55224600-55228000	Enhancers	Primary T helper cells fromperipheralblood	blood
30	chr2:55224600-55229400	Enhancers	Breast Myoepithelial Primary Cells	Breast
31	chr2:55224800-55227800	Enhancers	NHLF	lung
32	chr2:55224800-55229000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
33	chr2:55224800-55229000	Enhancers	Fetal Heart	heart
34	chr2:55224800-55230200	Enhancers	Muscle Satellite Cultured Cells	--
35	chr2:55224800-55231000	Weak transcription	Small Intestine	intestine
36	chr2:55224800-55236800	Enhancers	A549	lung
37	chr2:55225000-55227600	Enhancers	Primary monocytes fromperipheralblood	blood
38	chr2:55225000-55227600	Enhancers	HSMMtube	muscle
39	chr2:55225000-55228000	Enhancers	Brain Hippocampus Middle	brain
40	chr2:55225000-55228400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr2:55225000-55228400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:55225000-55228400	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr2:55225200-55227400	Enhancers	Fetal Brain Male	brain
44	chr2:55225200-55234600	Enhancers	Liver	Liver
45	chr2:55225600-55227800	Enhancers	HMEC	breast
46	chr2:55225600-55227800	Enhancers	NH-A	brain
47	chr2:55225600-55228800	Enhancers	HUES64 Cell Line	embryonic stem cell
48	chr2:55225800-55227400	Enhancers	Fetal Lung	lung
49	chr2:55225800-55227600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:55225800-55227600	Enhancers	Hela-S3	cervix

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