Variant report

Variant	rs460475
Chromosome Location	chr21:40224953-40224954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40224619..40227702-chr21:40232966..40234903,3	MCF-7	breast:
2	chr21:40223431..40225086-chr21:40277290..40280274,2	MCF-7	breast:
3	chr21:40218988..40223370-chr21:40223471..40227627,7	K562	blood:
4	chr21:40221988..40225135-chr21:40277085..40280385,3	MCF-7	breast:
5	chr21:40183745..40185634-chr21:40221836..40225935,3	K562	blood:
6	chr21:40211369..40213824-chr21:40223080..40225148,2	K562	blood:
7	chr21:40175995..40178465-chr21:40223341..40225406,3	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1534824	0.90[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1534825	0.90[CHB][hapmap];0.88[JPT][hapmap];0.89[ASN][1000 genomes]
rs1534826	0.89[ASN][1000 genomes]
rs2070529	0.82[GIH][hapmap]
rs2070530	0.82[GIH][hapmap]
rs2836696	0.90[CHB][hapmap];0.89[JPT][hapmap];0.87[ASN][1000 genomes]
rs2836698	0.86[CHB][hapmap];0.89[JPT][hapmap];0.86[ASN][1000 genomes]
rs2836699	0.87[ASN][1000 genomes]
rs2836701	0.90[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2836702	0.87[ASN][1000 genomes]
rs2836705	0.88[ASN][1000 genomes]
rs2836706	0.91[CEU][hapmap];0.90[CHB][hapmap];0.88[CHD][hapmap];0.93[GIH][hapmap];0.89[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2836707	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836708	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2836709	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs457705	0.80[GIH][hapmap];0.82[MEX][hapmap]
rs460982	0.80[GIH][hapmap]
rs461155	0.80[GIH][hapmap];0.82[MEX][hapmap]
rs462776	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs463452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467940	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs467985	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468094	0.81[ASN][1000 genomes]
rs468107	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468193	0.95[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468331	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468456	0.89[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468529	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468837	0.91[CEU][hapmap];0.90[CHB][hapmap];0.98[CHD][hapmap];0.93[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468849	0.95[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469180	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469303	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs469353	0.95[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7276587	0.87[ASN][1000 genomes]
rs7279564	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7283959	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][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	nsv1062425	chr21:40172471-40380976	Enhancers Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv544442	chr21:40172471-40380976	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs460475	MX1	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
2	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
3	chr21:40219800-40225200	Weak transcription	Osteobl	bone
4	chr21:40219800-40229000	Weak transcription	Right Atrium	heart
5	chr21:40220400-40225200	Weak transcription	NHDF-Ad	bronchial
6	chr21:40220400-40229000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr21:40221200-40226400	Enhancers	HUVEC	blood vessel
8	chr21:40221200-40229000	Weak transcription	Left Ventricle	heart
9	chr21:40221400-40225200	Weak transcription	Spleen	Spleen
10	chr21:40222400-40225200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr21:40222400-40225200	Weak transcription	Fetal Muscle Trunk	muscle
12	chr21:40222400-40225600	Weak transcription	Fetal Muscle Leg	muscle
13	chr21:40222400-40228200	Weak transcription	Fetal Heart	heart
14	chr21:40222800-40226200	Enhancers	K562	blood
15	chr21:40223200-40226400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr21:40223200-40226600	Enhancers	Hela-S3	cervix
17	chr21:40223400-40225000	Weak transcription	NH-A	brain
18	chr21:40223400-40226400	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr21:40223400-40226400	Enhancers	NHEK	skin
20	chr21:40223600-40226000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr21:40223600-40226200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr21:40223800-40225400	Weak transcription	Dnd41	blood
23	chr21:40224000-40226200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr21:40224400-40225800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr21:40224400-40226000	Enhancers	NHLF	lung
26	chr21:40224400-40226200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr21:40224400-40226400	Enhancers	HMEC	breast
28	chr21:40224600-40225600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr21:40224600-40225800	Enhancers	Breast Myoepithelial Primary Cells	Breast
30	chr21:40224600-40225800	Enhancers	HepG2	liver
31	chr21:40224800-40225200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr21:40224800-40225600	Weak transcription	Esophagus	oesophagus
33	chr21:40224800-40226200	Enhancers	A549	lung

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