Variant report

Variant	rs2823165
Chromosome Location	chr21:16594253-16594254
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16434791..16438927-chr21:16592548..16596753,6	MCF-7	breast:
2	chr21:16435852..16438238-chr21:16592639..16595685,3	MCF-7	breast:
3	chr21:16586940..16589372-chr21:16591214..16594501,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs11909130	0.85[ASN][1000 genomes]
rs12482026	0.87[ASN][1000 genomes]
rs12483396	0.93[ASN][1000 genomes]
rs12483484	0.96[ASN][1000 genomes]
rs13046557	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs13046821	0.99[ASN][1000 genomes]
rs13051325	0.98[ASN][1000 genomes]
rs13052858	0.96[ASN][1000 genomes]
rs2064040	0.81[CEU][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823149	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2823151	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2823154	0.82[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2823155	0.82[CEU][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2823160	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823161	0.81[CEU][hapmap];0.83[TSI][hapmap]
rs2823163	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823166	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823167	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823168	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2823169	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823172	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823173	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823174	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823175	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823176	0.99[ASN][1000 genomes]
rs2823177	0.81[CEU][hapmap]
rs2823178	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823179	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823180	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823181	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6517301	0.87[ASN][1000 genomes]
rs6517302	0.87[ASN][1000 genomes]
rs6517303	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7281303	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8131982	0.96[ASN][1000 genomes]
rs9808777	0.82[CEU][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	nsv587059	chr21:16588414-16600408	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823165	SAMSN1	cis	parietal	SCAN

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16591400-16595200	Enhancers	Primary hematopoietic stem cells	blood
2	chr21:16591600-16597400	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr21:16592000-16596400	Enhancers	A549	lung
4	chr21:16592200-16594800	Enhancers	Adipose Nuclei	Adipose
5	chr21:16592200-16596000	Enhancers	HepG2	liver
6	chr21:16592200-16597800	Enhancers	Hela-S3	cervix
7	chr21:16592400-16595200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr21:16592400-16596000	Enhancers	Liver	Liver
9	chr21:16592400-16597800	Enhancers	NHEK	skin
10	chr21:16592600-16595800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr21:16592600-16596200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr21:16592800-16594400	Weak transcription	GM12878-XiMat	blood
13	chr21:16592800-16594800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr21:16592800-16597400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr21:16593000-16594400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr21:16593000-16594400	Weak transcription	Psoas Muscle	Psoas
17	chr21:16593000-16595400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
18	chr21:16593000-16597600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr21:16593200-16595000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr21:16593200-16595400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr21:16593400-16597400	Enhancers	NHLF	lung
22	chr21:16593600-16594800	Enhancers	HUES48 Cell Line	embryonic stem cell
23	chr21:16593600-16594800	Enhancers	iPS-15b Cell Line	embryonic stem cell
24	chr21:16593600-16595400	Enhancers	ES-I3 Cell Line	embryonic stem cell
25	chr21:16593600-16595600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr21:16593600-16597800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr21:16593800-16597200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr21:16593800-16598000	Enhancers	HMEC	breast
29	chr21:16594000-16594800	Enhancers	HUES64 Cell Line	embryonic stem cell
30	chr21:16594000-16594800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
31	chr21:16594000-16594800	Enhancers	iPS-20b Cell Line	embryonic stem cell
32	chr21:16594000-16595000	Enhancers	HUES6 Cell Line	embryonic stem cell
33	chr21:16594000-16595400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr21:16594000-16595400	Enhancers	Skeletal Muscle Female	skeletal muscle
35	chr21:16594000-16597400	Enhancers	Muscle Satellite Cultured Cells	--
36	chr21:16594200-16594600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
37	chr21:16594200-16594600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
38	chr21:16594200-16594600	Enhancers	Monocytes-CD14+_RO01746	blood
39	chr21:16594200-16595000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr21:16594200-16595000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr21:16594200-16595000	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr21:16594200-16595200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
43	chr21:16594200-16595400	Enhancers	Primary neutrophils fromperipheralblood	blood
44	chr21:16594200-16595800	Enhancers	Cortex derived primary cultured neurospheres	brain
45	chr21:16594200-16597400	Enhancers	Osteobl	bone

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