Variant report

Variant	rs7584430
Chromosome Location	chr2:55241686-55241687
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	FOS	chr2:55241650-55241826	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:55240957..55243233-chr2:55273939..55276356,2	K562	blood:
2	chr2:55241176..55242945-chr2:55276344..55278140,2	MCF-7	breast:
3	chr2:55236989..55239116-chr2:55240470..55242602,2	K562	blood:

Variant related genes	Relation type
RTN4	TF binding region
RNU6-433P	TF binding region
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10174838	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10210840	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12464070	0.80[ASN][1000 genomes]
rs12477711	0.83[ASN][1000 genomes]
rs12713284	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13011689	0.81[EUR][1000 genomes]
rs13387751	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2015919	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2044291	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2255112	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2255393	0.84[ASN][1000 genomes]
rs2580765	0.88[EUR][1000 genomes]
rs2580772	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2580773	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2580776	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588510	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2588514	0.81[AMR][1000 genomes]
rs2588517	0.82[ASN][1000 genomes]
rs2588518	0.86[ASN][1000 genomes]
rs2588519	0.85[ASN][1000 genomes]
rs2588521	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2860453	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2902649	0.83[ASN][1000 genomes]
rs2919129	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2920893	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2968786	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2968787	0.81[ASN][1000 genomes]
rs2968793	0.81[EUR][1000 genomes]
rs2968795	0.81[EUR][1000 genomes]
rs2968804	0.87[ASN][1000 genomes]
rs2972075	0.80[EUR][1000 genomes]
rs2972097	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35631428	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35826668	0.85[ASN][1000 genomes]
rs3806570	0.87[ASN][1000 genomes]
rs4672005	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6545466	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6726158	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6755468	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6760429	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7340476	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562292	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs968998	0.83[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
rs7584430	RTN4	cis	Esophagus Mucosa	GTEx
rs7584430	RTN4	cis	Artery Tibial	GTEx
rs7584430	RTN4	cis	Nerve Tibial	GTEx
rs7584430	RTN4	cis	Adipose Subcutaneous	GTEx
rs7584430	RTN4	cis	Whole Blood	GTEx
rs7584430	RTN4	cis	Artery Aorta	GTEx
rs7584430	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs7584430	RTN4	cis	Thyroid	GTEx

Chromatin state (count:116 , 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	chr2:55234800-55244800	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr2:55234800-55246000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr2:55236800-55243400	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr2:55237000-55243600	Enhancers	ES-I3 Cell Line	embryonic stem cell
7	chr2:55237400-55242800	Enhancers	HSMMtube	muscle
8	chr2:55237600-55242000	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr2:55237600-55243600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr2:55237600-55246000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr2:55237600-55247800	Weak transcription	Left Ventricle	heart
12	chr2:55237600-55249600	Weak transcription	Gastric	stomach
13	chr2:55237600-55250200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr2:55237600-55258600	Weak transcription	Ovary	ovary
15	chr2:55237600-55272600	Weak transcription	Fetal Stomach	stomach
16	chr2:55237800-55242200	Enhancers	NHLF	lung
17	chr2:55237800-55242800	Enhancers	Brain Substantia Nigra	brain
18	chr2:55237800-55242800	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:55237800-55242800	Enhancers	Rectal Smooth Muscle	rectum
20	chr2:55237800-55243000	Enhancers	Brain Inferior Temporal Lobe	brain
21	chr2:55237800-55243400	Enhancers	Osteobl	bone
22	chr2:55237800-55243600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr2:55237800-55243600	Enhancers	Brain Hippocampus Middle	brain
24	chr2:55238000-55243000	Enhancers	Adipose Nuclei	Adipose
25	chr2:55238200-55245800	Weak transcription	Brain Germinal Matrix	brain
26	chr2:55238400-55242400	Enhancers	Liver	Liver
27	chr2:55238400-55242600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr2:55238400-55244600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
29	chr2:55238400-55249200	Weak transcription	Pancreas	Pancrea
30	chr2:55238400-55249600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
31	chr2:55238400-55250800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr2:55238400-55251200	Weak transcription	Psoas Muscle	Psoas
33	chr2:55238400-55252200	Weak transcription	Fetal Thymus	thymus
34	chr2:55238400-55252400	Weak transcription	Thymus	Thymus
35	chr2:55238400-55253200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr2:55239000-55241800	Enhancers	iPS-18 Cell Line	embryonic stem cell
37	chr2:55239200-55243000	Enhancers	Duodenum Smooth Muscle	Duodenum
38	chr2:55239200-55244600	Weak transcription	Primary B cells from cord blood	blood
39	chr2:55239200-55244800	Weak transcription	Fetal Muscle Leg	muscle
40	chr2:55239200-55247800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr2:55239400-55242400	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr2:55239400-55243200	Enhancers	Pancreatic Islets	Pancreatic Islet
43	chr2:55239400-55243400	Genic enhancers	HSMM	muscle
44	chr2:55239400-55244800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr2:55239400-55245000	Weak transcription	Primary B cells from peripheral blood	blood
46	chr2:55239600-55241800	Weak transcription	H1 Cell Line	embryonic stem cell
47	chr2:55239600-55242200	Weak transcription	Primary neutrophils fromperipheralblood	blood
48	chr2:55239600-55242400	Enhancers	HepG2	liver
49	chr2:55239600-55243600	Weak transcription	Aorta	Aorta
50	chr2:55239800-55242000	Enhancers	Brain Anterior Caudate	brain

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