Variant report

Variant	rs894961
Chromosome Location	chr2:55347472-55347473
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:55273963..55277742-chr2:55344682..55351127,9	K562	blood:
2	chr2:55275026..55277831-chr2:55345996..55347891,2	MCF-7	breast:
3	chr2:55346562..55348270-chr2:55453778..55456492,2	K562	blood:
4	chr2:55325626..55328074-chr2:55345685..55348277,2	K562	blood:
5	chr2:55339781..55342552-chr2:55346442..55349594,4	K562	blood:
6	chr2:55255186..55258524-chr2:55346221..55348339,3	K562	blood:
7	chr2:55276893..55279420-chr2:55345173..55348059,4	K562	blood:
8	chr2:55315563..55318504-chr2:55346291..55347986,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000115310	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs11674027	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1444262	0.82[ASN][1000 genomes]
rs2920855	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920856	0.82[ASN][1000 genomes]
rs2920867	0.89[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2968800	0.81[TSI][hapmap]
rs2968801	0.89[GIH][hapmap];0.80[MEX][hapmap];0.83[TSI][hapmap]
rs2968802	0.89[GIH][hapmap];0.80[MEX][hapmap];0.81[TSI][hapmap]
rs2972095	0.91[CHB][hapmap];0.95[JPT][hapmap];0.92[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522772	chr2:55347472-55349726	Enhancers Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs894961	RTN4	cis	Skin Sun Exposed Lower leg	GTEx
rs894961	C2orf63	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55337200-55351000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr2:55339400-55351000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr2:55340800-55348000	Enhancers	Brain Hippocampus Middle	brain
4	chr2:55340800-55348000	Enhancers	Brain Substantia Nigra	brain
5	chr2:55342400-55350200	Enhancers	Fetal Heart	heart
6	chr2:55344400-55350200	Enhancers	Brain Cingulate Gyrus	brain
7	chr2:55344400-55350600	Enhancers	Brain Inferior Temporal Lobe	brain
8	chr2:55344600-55348600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr2:55344600-55350000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:55345200-55349000	Enhancers	Primary hematopoietic stem cells	blood
11	chr2:55345400-55350200	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr2:55345400-55350200	Enhancers	Brain Angular Gyrus	brain
13	chr2:55345600-55348000	Enhancers	iPS-18 Cell Line	embryonic stem cell
14	chr2:55345600-55348000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr2:55345600-55348200	Enhancers	Primary B cells from cord blood	blood
16	chr2:55345600-55348200	Enhancers	Primary B cells from peripheral blood	blood
17	chr2:55345600-55348400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr2:55345600-55350200	Enhancers	Brain Germinal Matrix	brain
19	chr2:55345600-55350200	Enhancers	Monocytes-CD14+_RO01746	blood
20	chr2:55345600-55350400	Enhancers	Primary neutrophils fromperipheralblood	blood
21	chr2:55345800-55347600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
22	chr2:55345800-55347600	Enhancers	Osteobl	bone
23	chr2:55345800-55348400	Enhancers	HUES6 Cell Line	embryonic stem cell
24	chr2:55345800-55348400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr2:55345800-55348400	Enhancers	Fetal Thymus	thymus
26	chr2:55345800-55348600	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr2:55345800-55348600	Enhancers	Adipose Nuclei	Adipose
28	chr2:55345800-55348800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
29	chr2:55345800-55348800	Enhancers	NHDF-Ad	bronchial
30	chr2:55345800-55349000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr2:55346000-55347800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:55346000-55347800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr2:55346000-55347800	Enhancers	Spleen	Spleen
34	chr2:55346000-55348200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr2:55346000-55351600	Enhancers	Cortex derived primary cultured neurospheres	brain
36	chr2:55346200-55350000	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr2:55346400-55347800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
38	chr2:55346400-55348600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr2:55346400-55349600	Weak transcription	HUVEC	blood vessel
40	chr2:55346600-55347600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr2:55346600-55348000	Enhancers	GM12878-XiMat	blood
42	chr2:55346600-55348600	Flanking Active TSS	Muscle Satellite Cultured Cells	--
43	chr2:55346600-55350800	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr2:55346800-55347800	Enhancers	Right Atrium	heart
45	chr2:55346800-55348000	Enhancers	H1 Cell Line	embryonic stem cell
46	chr2:55346800-55348000	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr2:55346800-55348000	Enhancers	Colon Smooth Muscle	Colon
48	chr2:55346800-55348400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
49	chr2:55346800-55348400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
50	chr2:55346800-55348400	Enhancers	Duodenum Smooth Muscle	Duodenum

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