Variant report

Variant	rs468849
Chromosome Location	chr21:40219605-40219606
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:40218988..40223370-chr21:40223471..40227627,7	K562	blood:
2	chr21:40210912..40213065-chr21:40219265..40221347,3	K562	blood:
3	chr21:40176403..40178101-chr21:40218059..40219647,2	K562	blood:
4	chr21:40176601..40179515-chr21:40218059..40219886,2	K562	blood:

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

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

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

rs_ID	r²[population]
rs1534824	0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534825	0.95[CHB][hapmap];0.94[JPT][hapmap];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534826	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2070529	0.80[GIH][hapmap]
rs2070530	0.80[GIH][hapmap]
rs2836696	0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[ASN][1000 genomes]
rs2836698	0.91[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs2836699	0.91[ASN][1000 genomes]
rs2836701	0.95[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];0.94[JPT][hapmap];0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836702	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2836705	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836706	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2836707	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836708	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836709	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs457705	0.82[MEX][hapmap]
rs460475	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]
rs461155	0.82[MEX][hapmap]
rs462776	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs463452	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[YRI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467940	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];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs467985	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];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468094	0.84[ASN][1000 genomes]
rs468107	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs468193	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468331	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs468456	0.94[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468529	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs468837	0.83[ASW][hapmap];0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469180	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469303	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs469353	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs59427744	0.81[ASN][1000 genomes]
rs7276587	0.90[ASN][1000 genomes]
rs7279564	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7283959	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs468849	MX1	cis	cerebellum	SCAN
rs468849	NDUFB2	trans	cerebellum	SCAN

Chromatin state (count:38 , 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	chr21:40216400-40221200	Weak transcription	HUVEC	blood vessel
4	chr21:40219000-40219800	Enhancers	iPS-18 Cell Line	embryonic stem cell
5	chr21:40219000-40220400	Enhancers	Skeletal Muscle Male	skeletal muscle
6	chr21:40219000-40220400	Enhancers	NHEK	skin
7	chr21:40219200-40219800	Enhancers	H1 Cell Line	embryonic stem cell
8	chr21:40219200-40219800	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr21:40219200-40219800	Enhancers	Right Atrium	heart
10	chr21:40219200-40219800	Enhancers	Osteobl	bone
11	chr21:40219200-40220000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr21:40219200-40220000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr21:40219200-40220000	Enhancers	Placenta	Placenta
14	chr21:40219200-40220000	Enhancers	HMEC	breast
15	chr21:40219200-40220600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr21:40219200-40220600	Enhancers	Fetal Muscle Trunk	muscle
17	chr21:40219200-40220800	Enhancers	Liver	Liver
18	chr21:40219200-40221200	Enhancers	Fetal Stomach	stomach
19	chr21:40219200-40221200	Enhancers	Left Ventricle	heart
20	chr21:40219200-40222200	Enhancers	K562	blood
21	chr21:40219200-40222400	Enhancers	Fetal Heart	heart
22	chr21:40219200-40222400	Enhancers	Fetal Lung	lung
23	chr21:40219200-40222400	Enhancers	Fetal Muscle Leg	muscle
24	chr21:40219400-40219800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr21:40219400-40219800	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr21:40219400-40219800	Enhancers	iPS-20b Cell Line	embryonic stem cell
27	chr21:40219400-40219800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr21:40219400-40219800	Enhancers	Duodenum Smooth Muscle	Duodenum
29	chr21:40219400-40219800	Enhancers	HSMMtube	muscle
30	chr21:40219400-40220000	Enhancers	NH-A	brain
31	chr21:40219400-40220400	Enhancers	NHDF-Ad	bronchial
32	chr21:40219400-40220600	Enhancers	Colon Smooth Muscle	Colon
33	chr21:40219400-40220800	Enhancers	Rectal Smooth Muscle	rectum
34	chr21:40219400-40223400	Weak transcription	Aorta	Aorta
35	chr21:40219400-40224000	Weak transcription	Esophagus	oesophagus
36	chr21:40219600-40219800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr21:40219600-40219800	Enhancers	Hela-S3	cervix
38	chr21:40219600-40220400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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