Variant report

Variant	rs2972089
Chromosome Location	chr2:55336291-55336292
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:55273237..55280299-chr2:55335301..55344768,18	K562	blood:
2	chr2:55275064..55278271-chr2:55336145..55339086,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs2920864	0.87[EUR][1000 genomes]
rs2920865	0.86[EUR][1000 genomes]
rs2920866	0.81[EUR][1000 genomes]
rs2920867	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2920868	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs2920876	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968800	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2968801	0.87[CEU][hapmap];0.85[EUR][1000 genomes]
rs2968802	0.87[CEU][hapmap];0.87[EUR][1000 genomes]
rs2968808	0.81[AFR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2968809	0.90[ASN][1000 genomes]
rs2968817	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2968819	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34307608	0.88[EUR][1000 genomes]
rs61691827	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1006172	chr2:55322883-55340812	Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	esv3345871	chr2:55323717-55336931	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
3	esv3457756	chr2:55323755-55336917	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3457755	chr2:55323788-55336864	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	esv3457757	chr2:55323788-55336864	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
6	esv9883	chr2:55323841-55336774	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
7	nsv999212	chr2:55324276-55340812	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
8	nsv1004503	chr2:55324276-55343705	Enhancers Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
9	nsv997458	chr2:55324276-55344326	Enhancers Weak transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
10	nsv1013316	chr2:55324276-55345262	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972089	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55321600-55339400	Weak transcription	Thymus	Thymus
2	chr2:55321800-55336400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr2:55325200-55340400	Weak transcription	Gastric	stomach
4	chr2:55327800-55338600	Weak transcription	Lung	lung
5	chr2:55327800-55338600	Weak transcription	Rectal Mucosa Donor 31	rectum
6	chr2:55329000-55338600	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:55329600-55342600	Weak transcription	NHEK	skin
8	chr2:55329800-55336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr2:55330600-55338600	Weak transcription	Aorta	Aorta
10	chr2:55331200-55339000	Weak transcription	Dnd41	blood
11	chr2:55331800-55338600	Weak transcription	Fetal Thymus	thymus
12	chr2:55332000-55343400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:55332400-55338400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:55332400-55338400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:55332600-55337200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr2:55332800-55336600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr2:55332800-55337800	Enhancers	NHLF	lung
18	chr2:55332800-55338000	Enhancers	Hela-S3	cervix
19	chr2:55332800-55338400	Enhancers	HSMM	muscle
20	chr2:55332800-55338600	Enhancers	Osteobl	bone
21	chr2:55333000-55336400	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr2:55333000-55338600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
23	chr2:55333200-55337200	Enhancers	Fetal Heart	heart
24	chr2:55333200-55338600	Enhancers	NHDF-Ad	bronchial
25	chr2:55333200-55338800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:55333600-55338600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr2:55334000-55337000	Enhancers	Colon Smooth Muscle	Colon
28	chr2:55334000-55337000	Enhancers	Rectal Smooth Muscle	rectum
29	chr2:55334000-55337400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr2:55334000-55338600	Enhancers	Muscle Satellite Cultured Cells	--
31	chr2:55334000-55338600	Enhancers	Brain Hippocampus Middle	brain
32	chr2:55334200-55336400	Enhancers	Brain Substantia Nigra	brain
33	chr2:55334200-55337000	Enhancers	Duodenum Smooth Muscle	Duodenum
34	chr2:55334200-55338600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr2:55334400-55337600	Enhancers	Stomach Smooth Muscle	stomach
36	chr2:55334400-55340800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr2:55334600-55338400	Enhancers	HepG2	liver
38	chr2:55334800-55338600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr2:55334800-55339400	Enhancers	Pancreatic Islets	Pancreatic Islet
40	chr2:55335000-55336400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:55335000-55336400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr2:55335000-55337200	Weak transcription	Pancreas	Pancrea
43	chr2:55335000-55337600	Enhancers	Fetal Stomach	stomach
44	chr2:55335000-55339000	Weak transcription	Placenta Amnion	Placenta Amnion
45	chr2:55335200-55336400	Weak transcription	Stomach Mucosa	stomach
46	chr2:55335200-55337600	Enhancers	Fetal Muscle Leg	muscle
47	chr2:55335200-55338600	Enhancers	HSMMtube	muscle
48	chr2:55335200-55339000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
49	chr2:55335400-55341000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr2:55335600-55337400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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