Variant report

Variant	rs2364403
Chromosome Location	chr1:155927752-155927753
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	chr1:155919861..155921980-chr1:155927409..155929222,2	MCF-7	breast:
2	chr1:155926397..155928797-chr1:155930464..155932499,2	K562	blood:
3	chr1:155926416..155928811-chr1:155936912..155940499,3	K562	blood:
4	chr1:155925431..155929052-chr1:155938942..155941749,4	K562	blood:
5	chr1:155919232..155923454-chr1:155925537..155928294,6	K562	blood:
6	chr1:155910241..155913815-chr1:155925549..155931886,5	K562	blood:
7	chr1:155921230..155923744-chr1:155926059..155928194,3	K562	blood:
8	chr1:155926889..155928740-chr1:155934359..155936673,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000173080	Chromatin interaction
ENSG00000116584	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10796955	0.85[GIH][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap]
rs10908483	0.88[AFR][1000 genomes]
rs11264426	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[ASN][1000 genomes]
rs11585845	0.95[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.94[ASN][1000 genomes]
rs12037177	0.92[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs12080846	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12091273	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12091361	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12144175	0.90[AFR][1000 genomes]
rs12568523	0.89[CHB][hapmap];0.86[JPT][hapmap];0.91[YRI][hapmap]
rs1889532	0.81[MEX][hapmap]
rs2016251	0.85[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.86[MEX][hapmap];0.82[TSI][hapmap];0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs2282301	0.80[ASW][hapmap];0.85[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.80[AMR][1000 genomes]
rs2297649	0.89[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.84[TSI][hapmap];0.96[ASN][1000 genomes]
rs4661218	0.82[MEX][hapmap]
rs66466805	0.94[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs6667652	0.93[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.80[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs6696019	0.85[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes]
rs7534858	0.90[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs7545308	0.81[AFR][1000 genomes]
rs867548	0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs867549	0.80[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.82[LWK][hapmap];0.91[MEX][hapmap];0.94[MKK][hapmap];0.91[YRI][hapmap];0.81[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs867550	0.93[ASW][hapmap];0.90[CHB][hapmap];0.82[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.80[AMR][1000 genomes]
rs915181	0.93[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.91[MEX][hapmap];0.86[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs928596	0.82[MEX][hapmap]

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	nsv916198	chr1:155804210-156403997	Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	428 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Amyotrophic lateral sclerosis (age of onset)	22959728	GWAS catalog

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs2364403	ROBLD3	cis	parietal	SCAN
rs2364403	SPRR3	cis	parietal	SCAN
rs2364403	RIT1	Cis_1M	lymphoblastoid	RTeQTL
rs2364403	CRABP2	cis	parietal	SCAN
rs2364403	ARHGEF2	cis	multi-tissue	Pritchard
rs2364403	YY1AP1	cis	cerebellum	SCAN
rs2364403	RIT1	cis	cerebellum	SCAN

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:155905000-155945600	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr1:155911200-155940000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr1:155914800-155929600	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr1:155914800-155929800	Strong transcription	Fetal Stomach	stomach
5	chr1:155914800-155930200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr1:155914800-155931600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
7	chr1:155915200-155930600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:155915200-155936800	Strong transcription	Fetal Brain Female	brain
9	chr1:155915200-155937000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:155915800-155929600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr1:155915800-155929600	Strong transcription	HMEC	breast
12	chr1:155915800-155929800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr1:155915800-155929800	Strong transcription	HSMMtube	muscle
14	chr1:155915800-155930000	Strong transcription	Left Ventricle	heart
15	chr1:155915800-155930400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:155915800-155930400	Strong transcription	Osteobl	bone
17	chr1:155915800-155930600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr1:155915800-155931600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr1:155915800-155935200	Strong transcription	Brain Germinal Matrix	brain
20	chr1:155915800-155936600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:155916000-155930600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr1:155916000-155931400	Strong transcription	HUVEC	blood vessel
23	chr1:155916000-155937000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr1:155916200-155929800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr1:155916200-155929800	Strong transcription	Stomach Smooth Muscle	stomach
26	chr1:155916200-155930200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr1:155916200-155931600	Weak transcription	Right Atrium	heart
28	chr1:155916200-155932400	Strong transcription	Colon Smooth Muscle	Colon
29	chr1:155916200-155937000	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr1:155916400-155929000	Strong transcription	Placenta	Placenta
31	chr1:155916400-155929400	Strong transcription	Brain Cingulate Gyrus	brain
32	chr1:155916400-155930400	Strong transcription	Adipose Nuclei	Adipose
33	chr1:155916400-155930600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr1:155916400-155931800	Strong transcription	Lung	lung
35	chr1:155916400-155936200	Strong transcription	HUES6 Cell Line	embryonic stem cell
36	chr1:155916400-155936400	Strong transcription	H1 Cell Line	embryonic stem cell
37	chr1:155916400-155936600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr1:155916400-155937200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
39	chr1:155916400-155937400	Strong transcription	HUES48 Cell Line	embryonic stem cell
40	chr1:155916600-155930000	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr1:155916600-155932400	Strong transcription	Sigmoid Colon	Sigmoid Colon
42	chr1:155916600-155935800	Strong transcription	Fetal Intestine Small	intestine
43	chr1:155916600-155937000	Strong transcription	HUES64 Cell Line	embryonic stem cell
44	chr1:155916600-155937200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:155916800-155931600	Strong transcription	Colonic Mucosa	Colon
46	chr1:155916800-155932400	Strong transcription	Rectal Mucosa Donor 31	rectum
47	chr1:155916800-155937000	Strong transcription	Thymus	Thymus
48	chr1:155917000-155931800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr1:155917000-155937200	Strong transcription	Fetal Intestine Large	intestine
50	chr1:155917000-155939400	Strong transcription	Dnd41	blood

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