Variant report

Variant	rs1046183
Chromosome Location	chr2:73301817-73301818
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr2:73301708-73302334	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr2:73297000..73299065-chr2:73300438..73301965,2	MCF-7	breast:
2	chr2:73300909..73302911-chr2:73316133..73317647,2	K562	blood:
3	chr2:73300396..73302911-chr2:73315000..73317633,2	K562	blood:
4	chr2:73247423..73249390-chr2:73299554..73302236,2	K562	blood:

Variant related genes	Relation type
SFXN5	TF binding region
ENSG00000135631	Chromatin interaction
ENSG00000144040	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10496188	1.00[ASW][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap]
rs13404068	0.89[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17008541	0.89[JPT][hapmap]
rs17008565	0.85[JPT][hapmap]
rs17008579	0.95[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes]
rs17008608	0.95[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2421099	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3849393	0.90[JPT][hapmap];0.85[TSI][hapmap]
rs56931614	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56992198	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs57875548	0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs58469852	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs58617186	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs58649746	0.86[ASN][1000 genomes]
rs58659495	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59108557	0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59802755	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60341789	0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61652727	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62147726	0.88[AFR][1000 genomes]
rs62147727	0.90[AFR][1000 genomes]
rs62147728	0.86[AFR][1000 genomes]
rs62147735	0.81[AFR][1000 genomes]
rs62147756	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs66570372	0.83[AMR][1000 genomes]
rs6710911	0.90[JPT][hapmap];0.89[MEX][hapmap];0.85[TSI][hapmap]
rs6716846	0.81[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs67421457	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs6753054	0.84[JPT][hapmap]
rs6753133	0.89[JPT][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	nsv1002295	chr2:73216155-73350391	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1046183	ALMS1	cis	parietal	SCAN
rs1046183	CCT7	cis	cerebellum	SCAN
rs1046183	ALMS1	cis	cerebellum	SCAN
rs1046183	TGFA	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:73299200-73314800	Weak transcription	Small Intestine	intestine
2	chr2:73299400-73302000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr2:73299400-73302000	Weak transcription	Esophagus	oesophagus
4	chr2:73299400-73302000	Weak transcription	Ovary	ovary
5	chr2:73299400-73302200	Weak transcription	Lung	lung
6	chr2:73299400-73306800	Weak transcription	Fetal Brain Male	brain
7	chr2:73299400-73314800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
8	chr2:73299400-73314800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:73299400-73318200	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr2:73299400-73318400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:73299600-73302000	Weak transcription	H9 Cell Line	embryonic stem cell
12	chr2:73299600-73302000	Weak transcription	Brain Germinal Matrix	brain
13	chr2:73299600-73302000	Weak transcription	Right Ventricle	heart
14	chr2:73299600-73302000	Weak transcription	A549	lung
15	chr2:73299600-73302200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr2:73299600-73302200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr2:73299600-73302200	Weak transcription	Hela-S3	cervix
18	chr2:73299600-73302600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr2:73299600-73302800	Weak transcription	Brain Hippocampus Middle	brain
20	chr2:73299600-73303000	Weak transcription	Brain Inferior Temporal Lobe	brain
21	chr2:73299600-73305600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr2:73299600-73305600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr2:73299600-73306400	Weak transcription	Brain Anterior Caudate	brain
24	chr2:73299600-73306600	Weak transcription	Brain Angular Gyrus	brain
25	chr2:73299600-73306600	Weak transcription	Left Ventricle	heart
26	chr2:73299600-73307600	Weak transcription	Brain Cingulate Gyrus	brain
27	chr2:73299600-73307800	Weak transcription	HUES6 Cell Line	embryonic stem cell
28	chr2:73299600-73312600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr2:73299600-73314200	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:73299600-73314600	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr2:73299600-73314800	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr2:73299600-73315400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr2:73299600-73316000	Weak transcription	NHDF-Ad	bronchial
34	chr2:73299600-73319400	Weak transcription	K562	blood
35	chr2:73299800-73302000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr2:73299800-73302400	Weak transcription	Psoas Muscle	Psoas
37	chr2:73299800-73302400	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr2:73299800-73307600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr2:73299800-73308000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
40	chr2:73299800-73311200	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr2:73299800-73314800	Weak transcription	Brain Substantia Nigra	brain
42	chr2:73299800-73314800	Weak transcription	HSMM	muscle
43	chr2:73300000-73302000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr2:73300000-73302000	Weak transcription	Adipose Nuclei	Adipose
45	chr2:73300000-73302800	Weak transcription	HMEC	breast
46	chr2:73300000-73305400	Strong transcription	Osteobl	bone
47	chr2:73300000-73307800	Strong transcription	Placenta	Placenta
48	chr2:73300000-73308800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr2:73300000-73312200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr2:73300000-73319200	Weak transcription	Rectal Mucosa Donor 31	rectum

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