Variant report

No.	Distal block	Cell Line	Cell type
1	chr21:40723013..40725443-chr21:40734759..40737536,2	K562	blood:
2	chr21:40721702..40724513-chr21:40734759..40737368,2	K562	blood:
3	chr21:40734249..40737056-chr21:40740418..40743217,2	K562	blood:
4	chr21:40683276..40686079-chr21:40732739..40735690,3	MCF-7	breast:
5	chr21:40718884..40721288-chr21:40733126..40735648,3	MCF-7	breast:
6	chr21:40720107..40722634-chr21:40734285..40737035,2	K562	blood:
7	chr21:40730002..40733257-chr21:40733422..40737177,3	K562	blood:

Variant related genes	Relation type
ENSG00000185658	Chromatin interaction
ENSG00000205581	Chromatin interaction

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11911475	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12106311	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13433458	0.84[ASN][1000 genomes]
rs1554933	1.00[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs1554934	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs2239384	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2735313	0.82[ASN][1000 genomes]
rs2776311	0.83[JPT][hapmap]
rs2836990	1.00[CHB][hapmap];0.81[JPT][hapmap];0.88[ASN][1000 genomes]
rs2836994	0.83[CHB][hapmap]
rs2836998	0.81[YRI][hapmap]
rs2854727	0.83[GIH][hapmap];0.83[JPT][hapmap]
rs28550626	0.85[ASN][1000 genomes]
rs28629334	0.84[ASN][1000 genomes]
rs3761372	0.92[CHB][hapmap];0.81[JPT][hapmap];0.84[ASN][1000 genomes]
rs4818027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59805871	0.84[AFR][1000 genomes];0.93[ASN][1000 genomes]
rs6517522	0.83[JPT][hapmap]
rs7279434	0.84[ASN][1000 genomes]
rs741795	0.83[JPT][hapmap]
rs8132324	0.85[ASN][1000 genomes]
rs8132993	0.83[GIH][hapmap]
rs9974653	0.81[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs9983270	0.88[ASN][1000 genomes]
rs9983368	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9983594	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv913744	chr21:40670167-40757973	Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
2	nsv1059420	chr21:40684295-40745952	Flanking Active TSS Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	50 gene(s)	inside rSNPs	diseases
3	nsv1059868	chr21:40711535-41043291	Active TSS Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
4	esv2421785	chr21:40734723-40737012	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv442497	chr21:40734922-40737012	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS	Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2836992	HMGN1	cis	brain	seeQTL
rs2836992	HMGN1	cis	multi-tissue	Pritchard
rs2836992	WRB	cis	multi-tissue	Pritchard
rs2836992	WRB	cis	Artery Tibial	GTEx
rs2836992	WRB	cis	Adipose Subcutaneous	GTEx
rs2836992	BRWD1	cis	multi-tissue	Pritchard
rs2836992	HMGN1	trans	brain	seeQTL
rs2836992	SH3BGR	cis	Artery Tibial	GTEx
rs2836992	LOC643790	trans	multi-tissue	Pritchard
rs2836992	WRB	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:40734000-40736600	Enhancers	Primary hematopoietic stem cells short term culture	blood
2	chr21:40734000-40736800	Enhancers	Primary hematopoietic stem cells	blood
3	chr21:40734000-40737400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr21:40734400-40737800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
5	chr21:40734800-40736600	Enhancers	K562	blood
6	chr21:40734800-40738200	Enhancers	Primary neutrophils fromperipheralblood	blood
7	chr21:40735400-40735800	Enhancers	HUES6 Cell Line	embryonic stem cell
8	chr21:40735400-40735800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
9	chr21:40735400-40736400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr21:40735600-40735800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr21:40735600-40736000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr21:40735600-40736200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr21:40735600-40737000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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