Variant report

Variant	rs2580772
Chromosome Location	chr2:55218805-55218806
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:55218567-55218870	SK-N-SH	brain:	n/a	n/a
2	POLR2A	chr2:55218294-55219846	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55216168..55220754-chr2:55221880..55224884,4	MCF-7	breast:

Variant related genes	Relation type
RTN4	TF binding region

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

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

rs_ID	r²[population]
rs10174838	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210840	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11674808	0.82[EUR][1000 genomes]
rs12464070	0.86[ASN][1000 genomes]
rs12477711	0.88[ASN][1000 genomes]
rs12713284	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]
rs13011689	0.84[EUR][1000 genomes]
rs13387751	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]
rs2015919	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2044291	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255112	0.91[ASW][hapmap];0.82[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2255393	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs2580764	0.86[ASN][1000 genomes]
rs2580765	0.91[ASW][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2580773	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2580776	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2588510	1.00[ASW][hapmap];0.95[CHB][hapmap];0.83[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2588514	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2588517	1.00[CHB][hapmap];0.81[CHD][hapmap];0.92[ASN][1000 genomes]
rs2588518	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]
rs2588519	0.86[JPT][hapmap];0.80[ASN][1000 genomes]
rs2588521	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2860453	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902649	0.88[ASN][1000 genomes]
rs2919129	0.91[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap]
rs2920893	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2920900	0.82[EUR][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968787	0.85[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968790	0.82[EUR][1000 genomes]
rs2968793	0.83[EUR][1000 genomes]
rs2968794	0.96[CEU][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2968804	0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs2972072	0.92[CEU][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.82[EUR][1000 genomes]
rs2972075	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs2972090	0.95[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs2972097	0.96[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35631428	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35826668	0.92[ASN][1000 genomes]
rs3806570	0.92[ASN][1000 genomes]
rs4672005	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545466	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]
rs6726158	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6755468	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6760429	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]
rs7340476	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]
rs7562292	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]
rs7570629	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs7584430	0.88[AMR][1000 genomes];0.89[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
rs2580772	RTN4	cis	Artery Aorta	GTEx
rs2580772	RTN4	cis	Esophagus Mucosa	GTEx
rs2580772	RTN4	cis	Nerve Tibial	GTEx
rs2580772	RTN4	cis	Artery Tibial	GTEx
rs2580772	RTN4	cis	Adipose Subcutaneous	GTEx
rs2580772	RTN4	cis	Whole Blood	GTEx
rs2580772	RTN4	cis	Thyroid	GTEx
rs2580772	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:113 , 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	chr2:55203800-55222600	Weak transcription	Spleen	Spleen
5	chr2:55203800-55223800	Weak transcription	Pancreas	Pancrea
6	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
7	chr2:55205200-55220600	Weak transcription	Small Intestine	intestine
8	chr2:55205200-55223800	Weak transcription	Left Ventricle	heart
9	chr2:55210000-55228200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
10	chr2:55211200-55232000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr2:55212200-55220600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:55212600-55220200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
13	chr2:55212600-55226400	Weak transcription	Fetal Stomach	stomach
14	chr2:55213800-55226400	Weak transcription	Ovary	ovary
15	chr2:55214200-55224600	Weak transcription	Primary T cells from cord blood	blood
16	chr2:55214200-55225000	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr2:55214200-55234400	Weak transcription	Fetal Muscle Trunk	muscle
18	chr2:55214400-55222800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr2:55214400-55232800	Weak transcription	Fetal Brain Female	brain
20	chr2:55214600-55225600	Weak transcription	NH-A	brain
21	chr2:55214600-55226000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr2:55214800-55219000	Weak transcription	NHEK	skin
23	chr2:55214800-55219200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
24	chr2:55214800-55219200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr2:55214800-55220600	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr2:55214800-55221600	Weak transcription	HSMMtube	muscle
27	chr2:55214800-55221800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr2:55214800-55222000	Weak transcription	GM12878-XiMat	blood
29	chr2:55214800-55223600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr2:55214800-55223800	Weak transcription	Gastric	stomach
31	chr2:55214800-55224400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr2:55214800-55224400	Weak transcription	Rectal Mucosa Donor 31	rectum
33	chr2:55214800-55224600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr2:55214800-55225000	Weak transcription	Primary monocytes fromperipheralblood	blood
35	chr2:55214800-55225000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
36	chr2:55214800-55225200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr2:55214800-55225200	Weak transcription	Fetal Brain Male	brain
38	chr2:55214800-55225600	Weak transcription	Primary neutrophils fromperipheralblood	blood
39	chr2:55214800-55225600	Weak transcription	Brain Germinal Matrix	brain
40	chr2:55214800-55226000	Weak transcription	HUVEC	blood vessel
41	chr2:55214800-55226400	Weak transcription	Fetal Muscle Leg	muscle
42	chr2:55214800-55226400	Weak transcription	Fetal Thymus	thymus
43	chr2:55214800-55227200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr2:55214800-55227200	Weak transcription	HepG2	liver
45	chr2:55214800-55228800	Weak transcription	Fetal Intestine Large	intestine
46	chr2:55214800-55230600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
47	chr2:55214800-55231600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr2:55214800-55234200	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr2:55214800-55236800	Weak transcription	Primary T cells fromperipheralblood	blood
50	chr2:55215000-55219200	Weak transcription	HMEC	breast

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