Variant report

Variant	rs4472163
Chromosome Location	chr4:79626227-79626228
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79620166..79622821-chr4:79623905..79627089,5	K562	blood:
2	chr4:79624848..79626853-chr4:79632254..79635758,4	K562	blood:
3	chr4:79624162..79626279-chr4:79696304..79697859,2	K562	blood:
4	chr4:79624848..79628540-chr4:79632254..79635758,6	K562	blood:

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs10008008	0.93[EUR][1000 genomes]
rs10008069	0.85[CHB][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs10029214	0.81[TSI][hapmap]
rs10084949	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1134123	0.83[EUR][1000 genomes]
rs1134124	0.83[EUR][1000 genomes]
rs11724233	0.80[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[ASN][1000 genomes]
rs11931947	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs13101941	0.81[AMR][1000 genomes]
rs13101964	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13114489	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13133277	0.94[EUR][1000 genomes]
rs1346144	0.97[EUR][1000 genomes]
rs1346145	0.91[CEU][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes]
rs1469289	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1469290	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1582759	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1806906	0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs1834519	0.81[CEU][hapmap];0.82[GIH][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs1966537	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2867465	0.94[EUR][1000 genomes]
rs2867466	0.94[EUR][1000 genomes]
rs2903578	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4074675	0.80[EUR][1000 genomes]
rs4257676	0.88[CEU][hapmap];0.84[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes]
rs4264856	0.87[CEU][hapmap];0.85[CHB][hapmap];0.91[EUR][1000 genomes]
rs4321658	0.91[EUR][1000 genomes]
rs4365753	0.87[CEU][hapmap];0.85[CHB][hapmap];0.82[GIH][hapmap];0.80[JPT][hapmap];0.97[TSI][hapmap];0.91[EUR][1000 genomes]
rs4472162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4495064	0.84[TSI][hapmap]
rs4560439	0.87[CEU][hapmap];0.85[CHB][hapmap];0.80[JPT][hapmap];0.95[TSI][hapmap];0.91[EUR][1000 genomes]
rs4612	0.81[TSI][hapmap]
rs4619914	0.87[CEU][hapmap];0.84[CHB][hapmap];0.91[EUR][1000 genomes]
rs6533940	0.94[EUR][1000 genomes]
rs6533951	0.80[CEU][hapmap];0.95[CHB][hapmap];0.87[CHD][hapmap];0.95[JPT][hapmap];0.83[MEX][hapmap];0.81[TSI][hapmap];0.87[ASN][1000 genomes]
rs6818230	0.94[EUR][1000 genomes]
rs6825593	0.90[EUR][1000 genomes]
rs6842686	0.84[TSI][hapmap]
rs6842723	0.84[TSI][hapmap]
rs6855458	0.82[CEU][hapmap];0.97[TSI][hapmap];0.90[EUR][1000 genomes]
rs7672208	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7677162	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7694971	0.82[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699519	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7699905	0.93[EUR][1000 genomes]
rs9992088	0.81[EUR][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4472163	CXCL10	cis	parietal	SCAN
rs4472163	LOC643424	cis	multi-tissue	Pritchard
rs4472163	ANXA3	cis	cerebellum	SCAN

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79624800-79626800	Enhancers	K562	blood
2	chr4:79624800-79628800	Enhancers	Fetal Intestine Small	intestine
3	chr4:79625000-79628400	Weak transcription	Monocytes-CD14+_RO01746	blood
4	chr4:79625800-79626600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:79625800-79626600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:79625800-79626600	Enhancers	NHDF-Ad	bronchial
7	chr4:79625800-79626600	Enhancers	NHEK	skin
8	chr4:79625800-79627000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr4:79625800-79627000	Enhancers	Cortex derived primary cultured neurospheres	brain
10	chr4:79625800-79627000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr4:79625800-79627000	Enhancers	Rectal Mucosa Donor 29	rectum
12	chr4:79625800-79627400	Enhancers	Small Intestine	intestine
13	chr4:79625800-79627600	Enhancers	Brain Angular Gyrus	brain
14	chr4:79625800-79628400	Enhancers	Brain Inferior Temporal Lobe	brain
15	chr4:79625800-79628800	Enhancers	Brain Anterior Caudate	brain
16	chr4:79625800-79628800	Enhancers	Fetal Intestine Large	intestine
17	chr4:79625800-79629400	Enhancers	Brain Substantia Nigra	brain
18	chr4:79626000-79626400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:79626000-79626400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr4:79626000-79626400	Enhancers	HMEC	breast
21	chr4:79626000-79626600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr4:79626000-79626600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr4:79626000-79626600	Enhancers	HSMMtube	muscle
24	chr4:79626000-79626600	Enhancers	NH-A	brain
25	chr4:79626000-79627200	Enhancers	Duodenum Mucosa	Duodenum
26	chr4:79626000-79627400	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr4:79626000-79627600	Enhancers	HUES48 Cell Line	embryonic stem cell
28	chr4:79626000-79627600	Enhancers	Placenta Amnion	Placenta Amnion
29	chr4:79626000-79627600	Enhancers	HSMM	muscle
30	chr4:79626000-79628400	Enhancers	Brain Cingulate Gyrus	brain
31	chr4:79626000-79628800	Enhancers	H9 Cell Line	embryonic stem cell
32	chr4:79626000-79628800	Enhancers	Fetal Heart	heart
33	chr4:79626000-79629400	Enhancers	H1 Cell Line	embryonic stem cell
34	chr4:79626000-79629400	Enhancers	HUES6 Cell Line	embryonic stem cell
35	chr4:79626000-79629400	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr4:79626000-79629600	Enhancers	Primary B cells from peripheral blood	blood
37	chr4:79626000-79629600	Enhancers	Brain Hippocampus Middle	brain
38	chr4:79626200-79626400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
39	chr4:79626200-79626400	Flanking Active TSS	HepG2	liver
40	chr4:79626200-79626600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr4:79626200-79626600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr4:79626200-79626800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr4:79626200-79627000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr4:79626200-79627200	Enhancers	Rectal Mucosa Donor 31	rectum
45	chr4:79626200-79627600	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr4:79626200-79629200	Enhancers	HUES64 Cell Line	embryonic stem cell
47	chr4:79626200-79629400	Enhancers	iPS-18 Cell Line	embryonic stem cell

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