Variant report

Variant	rs6533821
Chromosome Location	chr4:79524420-79524421
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr4:79520729..79523356-chr4:79524267..79526444,2	K562	blood:
2	chr4:79522884..79525832-chr4:79695803..79698616,2	K562	blood:
3	chr4:79514162..79516035-chr4:79524140..79525956,2	K562	blood:
4	chr4:79522193..79524527-chr4:79697309..79699707,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260278	Chromatin interaction
ENSG00000138772	Chromatin interaction
ENSG00000138756	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10001246	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10212636	0.84[EUR][1000 genomes]
rs1107606	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1108907	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11724268	0.90[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap]
rs11724602	0.84[EUR][1000 genomes]
rs11733032	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs11733269	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11736376	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs11736602	0.90[CEU][hapmap];0.88[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap]
rs11942573	0.81[CEU][hapmap];0.87[MEX][hapmap]
rs12233694	0.90[CEU][hapmap]
rs12641838	0.82[CHD][hapmap]
rs12642521	0.82[CHD][hapmap]
rs12643488	0.84[EUR][1000 genomes]
rs12646646	0.82[EUR][1000 genomes]
rs12711032	0.81[CEU][hapmap]
rs13120630	0.81[CEU][hapmap];0.83[MEX][hapmap]
rs13138005	0.90[CEU][hapmap];0.85[TSI][hapmap];0.86[EUR][1000 genomes]
rs1472365	0.82[CHD][hapmap]
rs1587222	0.82[CHD][hapmap];0.93[JPT][hapmap]
rs1874486	0.82[CHD][hapmap]
rs1874487	0.82[CHD][hapmap]
rs1972024	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3805174	0.82[CHD][hapmap]
rs4306980	0.90[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4353930	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs4466067	0.82[CHD][hapmap]
rs4975148	0.83[EUR][1000 genomes]
rs6533804	0.82[CHD][hapmap]
rs6533825	0.90[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6533835	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6533842	0.90[CEU][hapmap];0.91[GIH][hapmap];0.83[MEX][hapmap];0.85[TSI][hapmap];0.82[EUR][1000 genomes]
rs6533847	0.90[CEU][hapmap]
rs6811335	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6824014	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6829061	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6829198	0.84[EUR][1000 genomes]
rs6834587	0.90[CEU][hapmap];0.84[EUR][1000 genomes]
rs6835210	0.94[CEU][hapmap]
rs6835998	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6838443	0.81[CEU][hapmap]
rs6840592	0.90[CEU][hapmap]
rs6841654	0.90[CEU][hapmap]
rs6845893	0.81[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap]
rs6846346	0.84[EUR][1000 genomes]
rs6854055	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7317	0.90[CEU][hapmap];0.87[GIH][hapmap];0.85[TSI][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7656476	0.82[CHD][hapmap]
rs7657082	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7677783	0.80[CEU][hapmap]
rs7680749	0.84[EUR][1000 genomes]
rs7680766	0.90[CEU][hapmap];0.91[GIH][hapmap];0.87[MEX][hapmap];0.85[TSI][hapmap];0.84[EUR][1000 genomes]
rs7683399	0.82[CHD][hapmap]
rs7689154	0.84[EUR][1000 genomes]
rs950699	0.82[CHD][hapmap]
rs9998136	0.82[CEU][hapmap];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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
2	nsv967949	chr4:79511515-79527707	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6533821	CXCL10	cis	parietal	SCAN
rs6533821	ANXA3	cis	cerebellum	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:79474400-79527200	Weak transcription	Spleen	Spleen
2	chr4:79483000-79530000	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr4:79488400-79527400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr4:79490800-79532600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr4:79491000-79529600	Weak transcription	Aorta	Aorta
6	chr4:79491200-79535400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr4:79491800-79533200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:79491800-79542600	Weak transcription	NH-A	brain
9	chr4:79492000-79531600	Strong transcription	HMEC	breast
10	chr4:79502200-79529200	Weak transcription	Colonic Mucosa	Colon
11	chr4:79502400-79525800	Weak transcription	Psoas Muscle	Psoas
12	chr4:79502400-79532200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr4:79508200-79533600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr4:79508800-79525400	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr4:79508800-79527000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr4:79508800-79527400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr4:79512600-79534200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr4:79512600-79536800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr4:79512800-79525600	Weak transcription	NHLF	lung
20	chr4:79513800-79534200	Strong transcription	NHEK	skin
21	chr4:79516000-79525400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr4:79517200-79534800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
23	chr4:79518000-79548000	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr4:79518400-79528200	Strong transcription	Fetal Intestine Large	intestine
25	chr4:79518600-79543600	Weak transcription	Stomach Mucosa	stomach
26	chr4:79519200-79528400	Strong transcription	HUES6 Cell Line	embryonic stem cell
27	chr4:79521200-79527600	Weak transcription	Skeletal Muscle Male	skeletal muscle
28	chr4:79521400-79529800	Weak transcription	Primary hematopoietic stem cells	blood
29	chr4:79521400-79534000	Weak transcription	Right Ventricle	heart
30	chr4:79522200-79526600	Strong transcription	HUES64 Cell Line	embryonic stem cell
31	chr4:79522200-79529600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
32	chr4:79522600-79531200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr4:79522600-79531600	Weak transcription	HSMMtube	muscle
34	chr4:79523400-79525200	Strong transcription	Placenta Amnion	Placenta Amnion
35	chr4:79523600-79524600	Strong transcription	Adipose Nuclei	Adipose
36	chr4:79523600-79525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr4:79523600-79533800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr4:79523800-79528800	Strong transcription	Stomach Smooth Muscle	stomach
39	chr4:79524000-79525400	Strong transcription	Duodenum Smooth Muscle	Duodenum
40	chr4:79524000-79527200	Weak transcription	Left Ventricle	heart
41	chr4:79524000-79528200	Weak transcription	Colon Smooth Muscle	Colon
42	chr4:79524200-79524800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
43	chr4:79524200-79525000	Enhancers	K562	blood
44	chr4:79524200-79526400	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr4:79524200-79526800	Weak transcription	Fetal Intestine Small	intestine
46	chr4:79524200-79526800	Weak transcription	Fetal Stomach	stomach
47	chr4:79524200-79526800	Weak transcription	Gastric	stomach
48	chr4:79524200-79527000	Weak transcription	Esophagus	oesophagus
49	chr4:79524200-79527000	Weak transcription	Lung	lung
50	chr4:79524200-79527200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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