Variant report

Variant	rs1534827
Chromosome Location	chr21:40210618-40210619
allele	A/C
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:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:40207571..40212513-chr21:40281866..40285274,6	MCF-7	breast:
2	chr21:40203275..40206794-chr21:40210041..40212530,5	MCF-7	breast:
3	chr21:40176595..40179182-chr21:40208823..40211776,3	K562	blood:
4	chr21:40175934..40178688-chr21:40209789..40212200,2	MCF-7	breast:
5	chr21:40208198..40210644-chr21:40213695..40215361,2	K562	blood:
6	chr21:40205616..40208986-chr21:40210258..40212560,3	MCF-7	breast:
7	chr21:40209144..40212226-chr21:40213678..40216387,3	K562	blood:
8	chr21:40209378..40211862-chr21:40284823..40286804,2	MCF-7	breast:
9	chr21:40209482..40212563-chr21:40213470..40216289,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000157557	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs1009122	0.84[EUR][1000 genomes]
rs1009123	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11700716	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13047489	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13047716	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13048664	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1882734	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1893203	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs1893204	0.81[EUR][1000 genomes]
rs2015748	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2836697	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2836700	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2836703	1.00[CEU][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs374575	0.88[CEU][hapmap];0.88[EUR][1000 genomes]
rs455328	0.88[CEU][hapmap];0.83[EUR][1000 genomes]
rs456574	0.91[EUR][1000 genomes]
rs464366	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs464476	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs465657	0.88[CHB][hapmap]
rs468057	0.94[CEU][hapmap];1.00[CHB][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55938987	0.81[EUR][1000 genomes]
rs7276433	0.81[EUR][1000 genomes]
rs7279430	1.00[JPT][hapmap]
rs7281107	0.81[EUR][1000 genomes]
rs7281192	0.81[EUR][1000 genomes]
rs7281242	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs7281259	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7281698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs877372	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs909103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[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

No data

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40195000-40212600	Weak transcription	Right Atrium	heart
2	chr21:40195200-40213800	Weak transcription	Fetal Kidney	kidney
3	chr21:40196400-40229000	Weak transcription	Right Ventricle	heart
4	chr21:40196600-40211000	Weak transcription	Pancreas	Pancrea
5	chr21:40197000-40211800	Weak transcription	Esophagus	oesophagus
6	chr21:40203800-40225200	Weak transcription	Psoas Muscle	Psoas
7	chr21:40205400-40211800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr21:40209600-40210800	Enhancers	K562	blood
9	chr21:40209800-40211000	Enhancers	Muscle Satellite Cultured Cells	--
10	chr21:40209800-40212200	Enhancers	HepG2	liver
11	chr21:40209800-40212200	Enhancers	HUVEC	blood vessel
12	chr21:40210000-40211400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr21:40210000-40212200	Enhancers	Placenta Amnion	Placenta Amnion
14	chr21:40210000-40212400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr21:40210000-40212800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr21:40210000-40214000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr21:40210000-40214000	Enhancers	NHEK	skin
18	chr21:40210000-40214200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr21:40210000-40214200	Enhancers	HMEC	breast
20	chr21:40210200-40211800	Weak transcription	Placenta	Placenta
21	chr21:40210200-40212200	Enhancers	Fetal Muscle Trunk	muscle
22	chr21:40210200-40212400	Enhancers	NHLF	lung
23	chr21:40210200-40212800	Enhancers	NHDF-Ad	bronchial
24	chr21:40210200-40213800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr21:40210400-40211000	Enhancers	A549	lung
26	chr21:40210400-40211000	Enhancers	Osteobl	bone
27	chr21:40210400-40212400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr21:40210400-40212400	Enhancers	HSMM	muscle
29	chr21:40210400-40212600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr21:40210400-40212800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr21:40210600-40210800	Enhancers	Spleen	Spleen
32	chr21:40210600-40210800	Flanking Active TSS	Hela-S3	cervix
33	chr21:40210600-40212000	Enhancers	Fetal Stomach	stomach
34	chr21:40210600-40212200	Enhancers	HSMMtube	muscle

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