Variant report

Variant	rs6755468
Chromosome Location	chr2:55240026-55240027
allele	A/C
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	chr2:55239286-55240050	U87	brain:	n/a	n/a
2	POLR2A	chr2:55222320-55241658	K562	blood:	n/a	n/a
3	TCF7L2	chr2:55239180-55240291	HEK293	kidney:	n/a	n/a
4	POLR2A	chr2:55238935-55240618	SK-N-SH	brain:	n/a	n/a
5	POLR2A	chr2:55239343-55240233	U87	brain:	n/a	n/a
6	TCF7L2	chr2:55239790-55240574	PANC-1	pancreas:	n/a	n/a
7	MYC	chr2:55239839-55240321	MCF10A-Er-Src	breast:	n/a	n/a
8	POLR2A	chr2:55239038-55240752	A549	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55238547..55240641-chr2:55252176..55254092,2	MCF-7	breast:
2	chr2:55239250..55241157-chr2:55276968..55279206,2	K562	blood:
3	chr2:55239258..55241140-chr2:55243082..55244742,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs10174838	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10210840	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11674808	0.85[EUR][1000 genomes]
rs12464070	0.85[ASN][1000 genomes]
rs12477711	0.88[ASN][1000 genomes]
rs12713284	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]
rs13011689	0.85[EUR][1000 genomes]
rs13387751	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]
rs2015919	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2044291	0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2255112	0.92[ASW][hapmap];0.82[CHB][hapmap];0.95[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2255393	0.86[JPT][hapmap]
rs2580765	0.92[ASW][hapmap];0.86[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.96[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2580772	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]
rs2580773	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2580776	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2588510	0.83[ASW][hapmap];0.95[CHB][hapmap];0.85[CHD][hapmap];0.87[GIH][hapmap];0.95[JPT][hapmap];0.83[LWK][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2588514	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2588517	1.00[CHB][hapmap];0.82[CHD][hapmap];0.82[JPT][hapmap];0.88[ASN][1000 genomes]
rs2588518	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]
rs2588519	0.82[JPT][hapmap]
rs2588521	1.00[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2860453	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2902649	0.88[ASN][1000 genomes]
rs2919129	0.92[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.91[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920878	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs2920893	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2920900	0.83[EUR][1000 genomes]
rs2968786	0.92[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2968787	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs2968790	0.84[EUR][1000 genomes]
rs2968793	0.85[EUR][1000 genomes]
rs2968794	0.96[CEU][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes]
rs2968795	0.96[CEU][hapmap];0.85[EUR][1000 genomes]
rs2968804	0.82[JPT][hapmap]
rs2972072	0.92[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs2972075	0.96[CEU][hapmap];0.84[EUR][1000 genomes]
rs2972090	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs2972097	0.96[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs35631428	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35826668	0.90[ASN][1000 genomes]
rs3806570	0.94[ASN][1000 genomes]
rs4672005	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6545466	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]
rs6726158	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6760429	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]
rs7340476	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]
rs7562292	0.96[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7570629	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AMR][1000 genomes]
rs7584430	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs968998	1.00[CHB][hapmap];0.82[JPT][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
rs6755468	RTN4	cis	Thyroid	GTEx
rs6755468	RTN4	cis	Nerve Tibial	GTEx
rs6755468	RTN4	cis	Artery Aorta	GTEx
rs6755468	RTN4	cis	Whole Blood	GTEx
rs6755468	RTN4	cis	Esophagus Mucosa	GTEx
rs6755468	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs6755468	RTN4	cis	Adipose Subcutaneous	GTEx
rs6755468	RTN4	cis	Artery Tibial	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55203800-55258400	Weak transcription	Esophagus	oesophagus
2	chr2:55232200-55244800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr2:55233200-55240400	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr2:55235600-55240600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:55236600-55241400	Enhancers	HUES48 Cell Line	embryonic stem cell
8	chr2:55236800-55240800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
11	chr2:55237200-55241600	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr2:55237400-55240800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
13	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
14	chr2:55237600-55240400	Weak transcription	Fetal Brain Male	brain
15	chr2:55237600-55240800	Enhancers	Colon Smooth Muscle	Colon
16	chr2:55237600-55241000	Enhancers	NH-A	brain
17	chr2:55237600-55241200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:55237600-55241400	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr2:55237600-55241400	Enhancers	Fetal Lung	lung
20	chr2:55237600-55241600	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
22	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
25	chr2:55237600-55249600	Weak transcription	Gastric	stomach
26	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr2:55237600-55258600	Weak transcription	Ovary	ovary
28	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
29	chr2:55237800-55240400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
30	chr2:55237800-55240400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:55237800-55240600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr2:55237800-55241000	Enhancers	Primary T helper naive cells from peripheral blood	blood
33	chr2:55237800-55241000	Enhancers	Primary T helper cells PMA-I stimulated	--
34	chr2:55237800-55241000	Enhancers	Brain Cingulate Gyrus	brain
35	chr2:55237800-55241200	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr2:55237800-55241200	Enhancers	Primary T killer memory cells from peripheral blood	blood
37	chr2:55237800-55241200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
38	chr2:55237800-55241200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr2:55237800-55241600	Enhancers	Duodenum Mucosa	Duodenum
40	chr2:55237800-55242200	Enhancers	NHLF	lung
41	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
42	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
43	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
44	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
45	chr2:55237800-55243400	Enhancers	Osteobl	bone
46	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
48	chr2:55238000-55241000	Enhancers	Primary hematopoietic stem cells	blood
49	chr2:55238000-55241200	Enhancers	GM12878-XiMat	blood
50	chr2:55238000-55241400	Enhancers	Primary T cells from cord blood	blood

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