Variant report

Variant	rs1123350
Chromosome Location	chr21:40204624-40204625
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40175881..40179455-chr21:40201702..40207885,11	MCF-7	breast:
2	chr21:40203844..40205524-chr21:40205560..40208541,2	K562	blood:
3	chr21:40203275..40206794-chr21:40210041..40212530,5	MCF-7	breast:
4	chr21:40202141..40208683-chr21:40214749..40222143,9	K562	blood:
5	chr21:40189822..40191337-chr21:40202443..40204626,2	MCF-7	breast:
6	chr21:40202074..40204721-chr21:40221926..40224763,2	MCF-7	breast:
7	chr21:40175294..40179502-chr21:40201748..40206259,10	K562	blood:
8	chr21:40175199..40185296-chr21:40201950..40208355,14	K562	blood:
9	chr21:40194153..40196064-chr21:40203698..40205702,2	K562	blood:
10	chr21:40203433..40205843-chr21:40286942..40289085,2	MCF-7	breast:
11	chr21:40203421..40205161-chr21:40207870..40210107,2	MCF-7	breast:
12	chr21:40196402..40199978-chr21:40201440..40206017,5	K562	blood:
13	chr21:40181095..40183169-chr21:40202885..40205120,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000234035	Chromatin interaction
ENSG00000229986	Chromatin interaction
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1000844	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009121	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1051420	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1051475	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1051476	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10854389	0.87[ASN][1000 genomes]
rs11088450	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088451	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11088452	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088453	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11088454	0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11254	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.90[MEX][hapmap];0.90[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11701191	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11701500	0.94[CHB][hapmap];0.87[CHD][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs11702403	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12481740	1.00[CHB][hapmap];0.93[JPT][hapmap];0.90[ASN][1000 genomes]
rs12482470	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12483746	1.00[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12627283	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13046853	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047133	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13047537	0.92[ASN][1000 genomes]
rs13047745	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13048035	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13050340	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1571707	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs2070531	0.88[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2142035	0.94[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs2836683	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836684	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2836685	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836686	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836687	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836688	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836689	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836690	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836691	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836692	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836693	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2836694	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs2836710	0.94[CHB][hapmap];0.87[JPT][hapmap];0.89[ASN][1000 genomes]
rs2836711	0.94[CHB][hapmap];0.84[CHD][hapmap];0.81[GIH][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs6517481	0.89[EUR][1000 genomes]
rs7276961	0.88[EUR][1000 genomes]
rs7282444	0.94[CHB][hapmap];0.86[CHD][hapmap];0.87[JPT][hapmap];0.91[ASN][1000 genomes]
rs7282723	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs762386	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][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]
rs762387	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[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]
rs9941892	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs998855	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[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
rs1123350	PCP4	cis	cerebellum	SCAN
rs1123350	MX1	cis	cerebellum	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
2	chr21:40195200-40204800	Weak transcription	Aorta	Aorta
3	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
4	chr21:40196400-40206600	Weak transcription	Gastric	stomach
5	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
6	chr21:40196600-40205000	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr21:40196600-40211000	Weak transcription	Pancreas	Pancrea
8	chr21:40197000-40211800	Weak transcription	Esophagus	oesophagus
9	chr21:40202600-40204800	Enhancers	Placenta	Placenta
10	chr21:40202600-40205400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr21:40202600-40205600	Enhancers	Primary monocytes fromperipheralblood	blood
12	chr21:40202600-40207600	Enhancers	HepG2	liver
13	chr21:40202800-40204800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:40202800-40204800	Enhancers	NHEK	skin
15	chr21:40202800-40205000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr21:40202800-40205000	Enhancers	K562	blood
17	chr21:40202800-40205200	Enhancers	Placenta Amnion	Placenta Amnion
18	chr21:40203200-40210600	Weak transcription	Spleen	Spleen
19	chr21:40203400-40204800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
20	chr21:40203800-40205000	Enhancers	Primary B cells from cord blood	blood
21	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
22	chr21:40204200-40206800	Weak transcription	Fetal Stomach	stomach
23	chr21:40204200-40209600	Weak transcription	Dnd41	blood
24	chr21:40204200-40210200	Weak transcription	NHLF	lung
25	chr21:40204400-40205400	Enhancers	Hela-S3	cervix
26	chr21:40204400-40205600	Enhancers	Primary neutrophils fromperipheralblood	blood
27	chr21:40204600-40205400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr21:40204600-40205400	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr21:40204600-40210000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr21:40204600-40210000	Weak transcription	HMEC	breast

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