Variant report

Variant	rs1472365
Chromosome Location	chr4:79503230-79503231
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:79502435..79504816-chr4:79510543..79512063,3	K562	blood:
2	chr4:79496427..79498196-chr4:79501762..79503461,2	K562	blood:

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs10003947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11098257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11733269	0.82[CHD][hapmap]
rs12509033	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12641838	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12642521	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13126934	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1587222	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];0.87[TSI][hapmap]
rs1587223	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1874486	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874487	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1874488	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1995062	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2867462	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3805174	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3805175	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4466067	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4975147	1.00[CHB][hapmap]
rs6533804	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6533821	0.82[CHD][hapmap]
rs6833514	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6851992	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7654600	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7656476	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7679218	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7682502	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7683582	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs867677	0.95[CEU][hapmap];1.00[CHB][hapmap];0.81[JPT][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs950699	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.99[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	nsv1009633	chr4:78887573-79652236	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1472365	CXCL10	cis	parietal	SCAN
rs1472365	ANXA3	cis	cerebellum	SCAN

Chromatin state (count:54 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
2	chr4:79481800-79521000	Weak transcription	Right Ventricle	heart
3	chr4:79482800-79505000	Weak transcription	Fetal Lung	lung
4	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr4:79488400-79505800	Weak transcription	Lung	lung
6	chr4:79488400-79508000	Weak transcription	Gastric	stomach
7	chr4:79488400-79523600	Weak transcription	Esophagus	oesophagus
8	chr4:79488400-79527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr4:79488600-79512200	Weak transcription	Rectal Mucosa Donor 29	rectum
10	chr4:79489200-79504400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr4:79489800-79513600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:79490000-79523400	Weak transcription	Colon Smooth Muscle	Colon
13	chr4:79490600-79505800	Weak transcription	Stomach Mucosa	stomach
14	chr4:79490600-79521000	Weak transcription	Fetal Heart	heart
15	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr4:79491000-79505600	Weak transcription	Placenta	Placenta
17	chr4:79491000-79506000	Weak transcription	Pancreas	Pancrea
18	chr4:79491000-79506000	Weak transcription	Sigmoid Colon	Sigmoid Colon
19	chr4:79491000-79507000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
20	chr4:79491000-79508000	Weak transcription	Adipose Nuclei	Adipose
21	chr4:79491000-79510200	Weak transcription	Skeletal Muscle Male	skeletal muscle
22	chr4:79491000-79512200	Weak transcription	Rectal Smooth Muscle	rectum
23	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
24	chr4:79491200-79505800	Strong transcription	NHEK	skin
25	chr4:79491200-79507600	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr4:79491400-79507600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr4:79491600-79504800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr4:79491600-79512000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr4:79491800-79542600	Weak transcription	NH-A	brain
32	chr4:79492000-79531600	Strong transcription	HMEC	breast
33	chr4:79495000-79503400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr4:79495600-79504400	Weak transcription	Left Ventricle	heart
35	chr4:79498600-79506000	Strong transcription	Fetal Intestine Small	intestine
36	chr4:79499600-79510800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr4:79500000-79505600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr4:79500000-79506000	Strong transcription	Fetal Intestine Large	intestine
39	chr4:79500000-79522200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr4:79500200-79509600	Strong transcription	Stomach Smooth Muscle	stomach
41	chr4:79500200-79510600	Strong transcription	Placenta Amnion	Placenta Amnion
42	chr4:79500400-79509200	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr4:79500800-79506000	Weak transcription	HUVEC	blood vessel
44	chr4:79501200-79503400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr4:79501400-79516000	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr4:79501800-79506400	Strong transcription	Fetal Stomach	stomach
47	chr4:79502200-79503600	Strong transcription	A549	lung
48	chr4:79502200-79510800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
49	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
50	chr4:79502400-79525800	Weak transcription	Psoas Muscle	Psoas

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