Variant report

Variant	rs2823169
Chromosome Location	chr21:16595099-16595100
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr21:16434791..16438927-chr21:16592548..16596753,6	MCF-7	breast:
2	chr21:16435852..16438238-chr21:16592639..16595685,3	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	0.84[ASN][1000 genomes]
rs12482026	0.86[ASN][1000 genomes]
rs12483396	0.92[ASN][1000 genomes]
rs12483484	0.96[ASN][1000 genomes]
rs13046557	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap]
rs13046821	0.98[ASN][1000 genomes]
rs13051325	0.97[ASN][1000 genomes]
rs13052858	0.95[ASN][1000 genomes]
rs2064040	0.81[CEU][hapmap];0.84[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs2823149	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2823151	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2823154	0.82[CEU][hapmap];0.81[CHD][hapmap];0.95[JPT][hapmap]
rs2823155	0.82[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs2823160	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823161	0.81[CEU][hapmap];0.81[TSI][hapmap]
rs2823163	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823165	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]
rs2823166	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823167	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823168	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2823172	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823173	0.82[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2823174	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2823175	0.82[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2823176	0.98[ASN][1000 genomes]
rs2823177	0.81[CEU][hapmap]
rs2823178	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2823179	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823180	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2823181	0.82[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6517301	0.86[ASN][1000 genomes]
rs6517302	0.86[ASN][1000 genomes]
rs6517303	0.82[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs7281303	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8131982	0.96[ASN][1000 genomes]
rs9808777	0.82[CEU][hapmap];0.81[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.80[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
rs2823169	SAMSN1	cis	parietal	SCAN

Chromatin state (count:49 , 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	chr21:16592200-16596000	Enhancers	HepG2	liver
5	chr21:16592200-16597800	Enhancers	Hela-S3	cervix
6	chr21:16592400-16595200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr21:16592400-16596000	Enhancers	Liver	Liver
8	chr21:16592400-16597800	Enhancers	NHEK	skin
9	chr21:16592600-16595800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr21:16592600-16596200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr21:16592800-16597400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr21:16593000-16595400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr21:16593000-16597600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr21:16593200-16595400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr21:16593400-16597400	Enhancers	NHLF	lung
16	chr21:16593600-16595400	Enhancers	ES-I3 Cell Line	embryonic stem cell
17	chr21:16593600-16595600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr21:16593600-16597800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr21:16593800-16597200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr21:16593800-16598000	Enhancers	HMEC	breast
21	chr21:16594000-16595400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr21:16594000-16595400	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr21:16594000-16597400	Enhancers	Muscle Satellite Cultured Cells	--
24	chr21:16594200-16595200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr21:16594200-16595400	Enhancers	Primary neutrophils fromperipheralblood	blood
26	chr21:16594200-16595800	Enhancers	Cortex derived primary cultured neurospheres	brain
27	chr21:16594200-16597400	Enhancers	Osteobl	bone
28	chr21:16594400-16595200	Enhancers	GM12878-XiMat	blood
29	chr21:16594400-16597400	Enhancers	NHDF-Ad	bronchial
30	chr21:16594400-16597800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr21:16594600-16595200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr21:16594600-16595200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
33	chr21:16594600-16597200	Weak transcription	Esophagus	oesophagus
34	chr21:16594800-16595200	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr21:16594800-16595800	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
36	chr21:16594800-16595800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
37	chr21:16594800-16595800	Weak transcription	Psoas Muscle	Psoas
38	chr21:16594800-16595800	Weak transcription	Right Ventricle	heart
39	chr21:16594800-16596000	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
40	chr21:16595000-16595400	Bivalent Enhancer	ES-WA7 Cell Line	embryonic stem cell
41	chr21:16595000-16595400	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
42	chr21:16595000-16595400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
43	chr21:16595000-16595400	Enhancers	Monocytes-CD14+_RO01746	blood
44	chr21:16595000-16595800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr21:16595000-16595800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
46	chr21:16595000-16596000	Bivalent Enhancer	iPS-20b Cell Line	embryonic stem cell
47	chr21:16595000-16596400	Weak transcription	NH-A	brain
48	chr21:16595000-16596600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
49	chr21:16595000-16597000	Weak transcription	HSMM	muscle

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