Variant report

Variant	rs2823146
Chromosome Location	chr21:16583736-16583737
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:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:11 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:16580196..16583993-chr21:16711928..16716549,7	MCF-7	breast:
2	chr21:16583537..16586474-chr21:16857105..16859617,2	MCF-7	breast:
3	chr21:16581111..16587442-chr21:16661859..16666667,10	MCF-7	breast:
4	chr21:16248533..16251618-chr21:16578938..16584306,4	MCF-7	breast:
5	chr21:16543363..16545459-chr21:16581109..16583907,2	MCF-7	breast:
6	chr21:16577077..16584288-chr21:16662087..16667374,8	MCF-7	breast:
7	chr21:16580777..16584780-chr21:16852967..16856651,5	MCF-7	breast:
8	chr21:16429926..16439498-chr21:16561851..16585948,113	MCF-7	breast:
9	chr21:16421751..16443998-chr21:16557859..16589610,273	MCF-7	breast:
10	chr21:16544983..16547085-chr21:16581063..16583747,4	MCF-7	breast:
11	chr21:16507551..16509625-chr21:16582039..16584912,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction
ENSG00000236471	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs12106385	0.83[EUR][1000 genomes]
rs16979537	0.92[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16979542	1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57126985	0.83[EUR][1000 genomes]
rs62219002	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62219020	0.83[EUR][1000 genomes]
rs62219024	1.00[AMR][1000 genomes]
rs62219025	1.00[AMR][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	nsv1063385	chr21:16521617-16926212	Enhancers Weak transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv913413	chr21:16537728-16621859	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2823146	LCE1D	trans	lymphoblastoid	seeQTL
rs2823146	NRIP1	cis	lymphoblastoid	seeQTL
rs2823146	LAPTM4B	trans	lymphoblastoid	seeQTL

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16576200-16585600	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr21:16577600-16584000	Weak transcription	Right Ventricle	heart
3	chr21:16578400-16583800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr21:16579600-16584400	Enhancers	Hela-S3	cervix
5	chr21:16579600-16584800	Enhancers	Primary neutrophils fromperipheralblood	blood
6	chr21:16581000-16585400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr21:16582000-16584200	Enhancers	Adipose Nuclei	Adipose
8	chr21:16582400-16584400	Flanking Active TSS	Liver	Liver
9	chr21:16582400-16585400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr21:16582600-16583800	Flanking Active TSS	HepG2	liver
11	chr21:16582600-16584400	Enhancers	Fetal Intestine Small	intestine
12	chr21:16582800-16584400	Flanking Active TSS	A549	lung
13	chr21:16583000-16584000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr21:16583000-16584000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr21:16583000-16584000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr21:16583000-16584000	Weak transcription	Placenta	Placenta
17	chr21:16583000-16584000	Weak transcription	Pancreas	Pancrea
18	chr21:16583000-16584000	Weak transcription	Psoas Muscle	Psoas
19	chr21:16583000-16584000	Weak transcription	Right Atrium	heart
20	chr21:16583000-16584000	Weak transcription	Spleen	Spleen
21	chr21:16583200-16584000	Enhancers	Primary hematopoietic stem cells	blood
22	chr21:16583400-16583800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr21:16583400-16585400	Enhancers	Primary B cells from cord blood	blood
24	chr21:16583600-16584000	Active TSS	Fetal Intestine Large	intestine
25	chr21:16583600-16584200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr21:16583600-16584200	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr21:16583600-16584400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
28	chr21:16583600-16585400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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