Variant report

Variant	rs2968817
Chromosome Location	chr2:55331982-55331983
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55322759..55325369-chr2:55329915..55332847,3	MCF-7	breast:
2	chr2:55331372..55335609-chr2:55337059..55340698,6	K562	blood:
3	chr2:55317970..55321435-chr2:55328777..55332297,3	K562	blood:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs2920864	0.84[EUR][1000 genomes]
rs2920865	0.83[EUR][1000 genomes]
rs2920867	0.84[EUR][1000 genomes]
rs2920868	0.84[EUR][1000 genomes]
rs2920876	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2968800	0.84[EUR][1000 genomes]
rs2968801	0.83[EUR][1000 genomes]
rs2968802	0.84[EUR][1000 genomes]
rs2968808	0.85[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2968809	0.92[ASN][1000 genomes]
rs2968819	1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2972089	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs34307608	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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
11	esv2421886	chr2:55324288-55335045	Enhancers Flanking Active TSS Weak transcription Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	esv3693301	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv517331	chr2:55324960-55335045	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
14	nsv817951	chr2:55324960-55335045	Weak transcription Enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
15	nsv438350	chr2:55327091-55333235	Enhancers Weak transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2968817	RTN4	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

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	chr2:55326800-55334600	Weak transcription	Brain Angular Gyrus	brain
5	chr2:55327800-55334600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr2:55327800-55335400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr2:55327800-55338600	Weak transcription	Lung	lung
8	chr2:55327800-55338600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr2:55328000-55333200	Weak transcription	Fetal Heart	heart
10	chr2:55328000-55334200	Weak transcription	Brain Substantia Nigra	brain
11	chr2:55328800-55334200	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr2:55329000-55338600	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr2:55329600-55332800	Weak transcription	A549	lung
14	chr2:55329600-55332800	Weak transcription	NHLF	lung
15	chr2:55329600-55333400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr2:55329600-55342600	Weak transcription	NHEK	skin
17	chr2:55329800-55332800	Weak transcription	Hela-S3	cervix
18	chr2:55329800-55332800	Weak transcription	K562	blood
19	chr2:55329800-55333000	Weak transcription	NH-A	brain
20	chr2:55329800-55334000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr2:55329800-55336600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr2:55330000-55332800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr2:55330000-55332800	Weak transcription	HSMM	muscle
24	chr2:55330200-55332000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr2:55330200-55332800	Weak transcription	Osteobl	bone
26	chr2:55330200-55334000	Weak transcription	HSMMtube	muscle
27	chr2:55330200-55334600	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:55330400-55333000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr2:55330600-55332600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr2:55330600-55333000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr2:55330600-55334000	Weak transcription	Rectal Smooth Muscle	rectum
32	chr2:55330600-55334400	Weak transcription	Stomach Smooth Muscle	stomach
33	chr2:55330600-55336000	Weak transcription	Adipose Nuclei	Adipose
34	chr2:55330600-55338600	Weak transcription	Aorta	Aorta
35	chr2:55330800-55332800	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:55330800-55333200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr2:55330800-55333200	Weak transcription	NHDF-Ad	bronchial
38	chr2:55330800-55333400	Weak transcription	Colon Smooth Muscle	Colon
39	chr2:55330800-55336000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr2:55331000-55334000	Weak transcription	HUVEC	blood vessel
41	chr2:55331200-55332400	Enhancers	Primary monocytes fromperipheralblood	blood
42	chr2:55331200-55332400	Enhancers	Monocytes-CD14+_RO01746	blood
43	chr2:55331200-55332800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr2:55331200-55332800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr2:55331200-55339000	Weak transcription	Dnd41	blood
46	chr2:55331400-55332000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr2:55331800-55338600	Weak transcription	Fetal Thymus	thymus

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