Variant report

Variant	rs6545462
Chromosome Location	chr2:55184444-55184445
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55183331..55185244-chr2:55275914..55277791,2	MCF-7	breast:
2	chr2:55164082..55167109-chr2:55181433..55184478,3	K562	blood:
3	chr2:55183507..55185896-chr2:55194020..55195726,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction
ENSG00000214595	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10179594	0.82[CEU][hapmap]
rs10196667	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10198636	0.96[EUR][1000 genomes]
rs10205017	0.85[EUR][1000 genomes]
rs10746530	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11125551	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11904457	0.93[ASN][1000 genomes]
rs12475185	0.93[ASN][1000 genomes]
rs12989576	1.00[CEU][hapmap];0.84[CHB][hapmap];0.83[EUR][1000 genomes]
rs13002841	1.00[CEU][hapmap]
rs13008105	0.93[ASN][1000 genomes]
rs13020490	0.97[ASN][1000 genomes]
rs13023202	0.82[EUR][1000 genomes]
rs13026576	0.97[ASN][1000 genomes]
rs13028800	0.93[ASN][1000 genomes]
rs17417648	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs17418111	0.93[ASN][1000 genomes]
rs2116491	0.82[CHB][hapmap];0.82[JPT][hapmap]
rs2580766	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2588520	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2919125	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2920863	0.82[CEU][hapmap];0.80[JPT][hapmap]
rs2920883	0.82[CEU][hapmap]
rs2920884	0.82[CEU][hapmap]
rs2920897	0.82[CEU][hapmap]
rs2968789	0.82[CEU][hapmap]
rs36024305	0.93[ASN][1000 genomes]
rs36063689	0.88[ASN][1000 genomes]
rs4233956	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4504034	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4525735	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4671233	0.90[ASN][1000 genomes]
rs4671998	0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs55777421	0.97[ASN][1000 genomes]
rs67721747	0.93[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	nsv582029	chr2:55159043-55204498	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6545462	RTN4	cis	Thyroid	GTEx

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55168800-55193400	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55170400-55190400	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr2:55173000-55193400	Weak transcription	Aorta	Aorta
4	chr2:55173200-55187000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr2:55173200-55203400	Weak transcription	Gastric	stomach
6	chr2:55173400-55184600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr2:55173600-55194000	Weak transcription	Stomach Smooth Muscle	stomach
8	chr2:55173600-55195000	Weak transcription	Pancreas	Pancrea
9	chr2:55174800-55194000	Weak transcription	Brain Germinal Matrix	brain
10	chr2:55175400-55193200	Weak transcription	Fetal Brain Female	brain
11	chr2:55175600-55185600	Weak transcription	Brain Inferior Temporal Lobe	brain
12	chr2:55175600-55185800	Weak transcription	Brain Cingulate Gyrus	brain
13	chr2:55175600-55185800	Weak transcription	Brain Substantia Nigra	brain
14	chr2:55175600-55194600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
15	chr2:55175800-55184600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr2:55175800-55193800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr2:55176400-55184600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
18	chr2:55177800-55193800	Weak transcription	Cortex derived primary cultured neurospheres	brain
19	chr2:55178200-55193400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr2:55178600-55193400	Weak transcription	Spleen	Spleen
21	chr2:55180400-55189600	Weak transcription	HSMMtube	muscle
22	chr2:55180600-55191600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr2:55180600-55193600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr2:55180600-55195400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr2:55180600-55196000	Weak transcription	NH-A	brain
26	chr2:55180800-55191200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:55181400-55184600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
28	chr2:55181600-55193600	Weak transcription	Lung	lung
29	chr2:55181600-55203400	Weak transcription	Ovary	ovary
30	chr2:55182200-55184600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:55182200-55185600	Weak transcription	Brain Hippocampus Middle	brain
32	chr2:55182400-55186600	Enhancers	Fetal Muscle Leg	muscle
33	chr2:55182800-55185800	Weak transcription	Brain Anterior Caudate	brain
34	chr2:55183000-55185000	Enhancers	iPS-18 Cell Line	embryonic stem cell
35	chr2:55183000-55191600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr2:55183000-55191600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr2:55183000-55192000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
38	chr2:55183200-55185800	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr2:55183200-55193200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
40	chr2:55183200-55193200	Weak transcription	NHLF	lung
41	chr2:55183200-55206800	Weak transcription	Stomach Mucosa	stomach
42	chr2:55183400-55184800	Enhancers	HUES48 Cell Line	embryonic stem cell
43	chr2:55183400-55184800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
44	chr2:55183400-55185000	Enhancers	iPS-20b Cell Line	embryonic stem cell
45	chr2:55183400-55196600	Weak transcription	Duodenum Smooth Muscle	Duodenum
46	chr2:55183600-55185000	Enhancers	ES-I3 Cell Line	embryonic stem cell
47	chr2:55183800-55185800	Weak transcription	Primary hematopoietic stem cells	blood
48	chr2:55183800-55185800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr2:55183800-55186600	Enhancers	K562	blood
50	chr2:55183800-55190400	Weak transcription	HepG2	liver

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