Variant report

Variant	rs2823139
Chromosome Location	chr21:16576783-16576784
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16575011..16578774-chr21:16661740..16665186,4	MCF-7	breast:
2	chr21:16429926..16439498-chr21:16561851..16585948,113	MCF-7	breast:
3	chr21:16495374..16497178-chr21:16575873..16578741,2	MCF-7	breast:
4	chr21:16421751..16443998-chr21:16557859..16589610,273	MCF-7	breast:
5	chr21:16576166..16576841-chr21:16816394..16817179,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000236471	Chromatin interaction
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1997595	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1997596	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2823131	0.86[ASW][hapmap];0.81[LWK][hapmap]
rs2823135	0.83[YRI][hapmap];0.81[AFR][1000 genomes]
rs2823136	0.83[YRI][hapmap]
rs2823138	0.94[ASW][hapmap];0.96[LWK][hapmap];0.84[MKK][hapmap];0.83[YRI][hapmap];0.90[AFR][1000 genomes]
rs2823140	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56038390	0.87[EUR][1000 genomes];0.81[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2823139	SAMSN1	cis	parietal	SCAN
rs2823139	TSSC4	trans	parietal	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16575200-16577000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
2	chr21:16575400-16576800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr21:16575400-16578000	Enhancers	Fetal Heart	heart
4	chr21:16575400-16579600	Enhancers	HepG2	liver
5	chr21:16576000-16577200	Enhancers	Primary hematopoietic stem cells	blood
6	chr21:16576000-16577400	Enhancers	A549	lung
7	chr21:16576000-16577600	Enhancers	Hela-S3	cervix
8	chr21:16576000-16577800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr21:16576000-16577800	Enhancers	Fetal Kidney	kidney
10	chr21:16576200-16577000	Enhancers	Fetal Intestine Large	intestine
11	chr21:16576200-16577600	Enhancers	K562	blood
12	chr21:16576200-16578200	Enhancers	Monocytes-CD14+_RO01746	blood
13	chr21:16576200-16585600	Enhancers	Primary monocytes fromperipheralblood	blood
14	chr21:16576400-16576800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr21:16576400-16576800	Enhancers	Fetal Intestine Small	intestine
16	chr21:16576400-16576800	Enhancers	Rectal Mucosa Donor 31	rectum
17	chr21:16576400-16577000	Enhancers	Fetal Lung	lung
18	chr21:16576400-16577000	Enhancers	Left Ventricle	heart
19	chr21:16576400-16577200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr21:16576400-16577800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr21:16576400-16577800	Enhancers	Fetal Muscle Leg	muscle
22	chr21:16576400-16578400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
23	chr21:16576400-16580000	Enhancers	Adipose Nuclei	Adipose
24	chr21:16576600-16577000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr21:16576600-16577400	Enhancers	Pancreas	Pancrea
26	chr21:16576600-16577400	Weak transcription	Right Ventricle	heart
27	chr21:16576600-16577800	Enhancers	Right Atrium	heart
28	chr21:16576600-16578000	Weak transcription	Liver	Liver

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