Variant report

Variant	rs4566333
Chromosome Location	chr2:172265747-172265748
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172260491..172264264-chr2:172264585..172267651,3	K562	blood:
2	chr2:172264138..172266023-chr2:172273310..172275434,2	K562	blood:
3	chr2:172264614..172267336-chr2:172269012..172271608,3	K562	blood:
4	chr2:172265528..172268533-chr2:172288621..172291396,3	MCF-7	breast:
5	chr2:172257799..172259945-chr2:172263821..172267063,3	K562	blood:
6	chr2:172261014..172263381-chr2:172264531..172266240,2	MCF-7	breast:
7	chr2:172265513..172268385-chr2:172270721..172272607,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000115827	Chromatin interaction
ENSG00000123600	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10171164	0.88[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs10177689	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10186304	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10192493	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10195398	0.92[CHD][hapmap]
rs10195990	1.00[CEU][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198915	0.86[AMR][1000 genomes]
rs10202883	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.83[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10210332	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13386613	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13388963	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13390534	0.85[CHD][hapmap]
rs13395084	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13396824	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13402901	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13414723	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13420838	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28608023	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28663293	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs57629676	0.83[AFR][1000 genomes]
rs58367130	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs58808521	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59235233	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59318451	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs59449823	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59599047	0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60523677	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62181354	0.94[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs6712098	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs73976149	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976150	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976153	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73976158	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs73976177	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7580497	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973419	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9973709	0.92[EUR][1000 genomes];1.00[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	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4566333	LOC440925	cis	lymphoblastoid	seeQTL
rs4566333	IFI44L	trans	lymphoblastoid	seeQTL

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172222200-172289600	Weak transcription	Gastric	stomach
2	chr2:172238000-172272400	Weak transcription	Fetal Intestine Large	intestine
3	chr2:172238800-172272400	Weak transcription	Primary T cells from cord blood	blood
4	chr2:172248000-172266000	Weak transcription	Left Ventricle	heart
5	chr2:172257000-172266000	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:172257600-172266000	Weak transcription	Aorta	Aorta
7	chr2:172258600-172272400	Weak transcription	A549	lung
8	chr2:172259400-172272200	Weak transcription	Fetal Intestine Small	intestine
9	chr2:172259800-172266000	Weak transcription	Esophagus	oesophagus
10	chr2:172260000-172271000	Weak transcription	K562	blood
11	chr2:172260200-172272200	Weak transcription	HepG2	liver
12	chr2:172261000-172266000	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:172261400-172266000	Weak transcription	Small Intestine	intestine
14	chr2:172261600-172265800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:172261600-172266000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr2:172261600-172266000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr2:172261600-172266000	Weak transcription	Dnd41	blood
18	chr2:172261600-172266000	Weak transcription	NHLF	lung
19	chr2:172261600-172266200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr2:172261600-172277800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr2:172261800-172265800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr2:172261800-172266000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr2:172261800-172266000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr2:172261800-172266000	Weak transcription	HSMM	muscle
25	chr2:172261800-172266000	Weak transcription	HUVEC	blood vessel
26	chr2:172261800-172266000	Weak transcription	NH-A	brain
27	chr2:172261800-172266000	Weak transcription	NHDF-Ad	bronchial
28	chr2:172262200-172265800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
29	chr2:172262200-172266000	Weak transcription	Hela-S3	cervix
30	chr2:172262400-172268800	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:172263200-172266000	Weak transcription	Primary T helper cells fromperipheralblood	blood
32	chr2:172264200-172266000	Enhancers	iPS-20b Cell Line	embryonic stem cell
33	chr2:172264200-172266000	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr2:172264200-172266000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
35	chr2:172264400-172266000	Weak transcription	Primary hematopoietic stem cells	blood
36	chr2:172264600-172266000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr2:172264800-172272400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
38	chr2:172265000-172272200	Weak transcription	Primary B cells from cord blood	blood
39	chr2:172265200-172265800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr2:172265200-172265800	Enhancers	NHEK	skin
41	chr2:172265200-172266000	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr2:172265200-172266000	Enhancers	HUES64 Cell Line	embryonic stem cell
43	chr2:172265200-172266000	Enhancers	iPS-15b Cell Line	embryonic stem cell
44	chr2:172265200-172266000	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr2:172265200-172267200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr2:172265400-172265800	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
47	chr2:172265400-172266000	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr2:172265400-172266000	Enhancers	HUES6 Cell Line	embryonic stem cell
49	chr2:172265400-172266000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr2:172265400-172266000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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