Variant report

Variant	rs2823106
Chromosome Location	chr21:16532660-16532661
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:16424737..16426720-chr21:16531523..16533319,2	MCF-7	breast:
2	chr21:16528404..16530433-chr21:16531935..16534391,2	K562	blood:
3	chr21:16434969..16437307-chr21:16530108..16533081,2	MCF-7	breast:
4	chr21:16532525..16534920-chr21:16535266..16536964,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000180530	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs11088311	0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12373912	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12482303	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12482386	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12482761	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12482834	0.95[ASN][1000 genomes]
rs12483016	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12483602	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1556283	1.00[CEU][hapmap];0.85[CHB][hapmap];0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882959	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1882963	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2007783	1.00[ASN][1000 genomes]
rs2008843	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2142362	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs2823086	0.87[ASN][1000 genomes]
rs2823088	0.95[ASN][1000 genomes]
rs2823091	1.00[ASN][1000 genomes]
rs2823093	1.00[ASN][1000 genomes]
rs2823096	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.92[MEX][hapmap];1.00[ASN][1000 genomes]
rs2823110	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823112	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.94[TSI][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823113	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823115	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823117	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823119	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2823123	1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2896680	1.00[ASN][1000 genomes]
rs2896689	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[GIH][hapmap];0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55778206	0.80[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55792425	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55797017	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55859143	0.95[ASN][1000 genomes]
rs62218221	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62218223	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62218224	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62218225	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62218995	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62218996	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs741937	1.00[ASN][1000 genomes]
rs8128132	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs990302	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2823106	TSSC4	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:16528000-16536600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr21:16528200-16536800	Weak transcription	Fetal Heart	heart
3	chr21:16530000-16535400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr21:16531000-16533400	Weak transcription	Pancreas	Pancrea
5	chr21:16531200-16533400	Enhancers	Primary B cells from peripheral blood	blood
6	chr21:16531400-16533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr21:16531400-16533600	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr21:16531400-16533600	Enhancers	Primary B cells from cord blood	blood
9	chr21:16531600-16533000	Enhancers	Fetal Intestine Small	intestine
10	chr21:16531600-16533000	Enhancers	Stomach Mucosa	stomach
11	chr21:16531600-16533000	Enhancers	GM12878-XiMat	blood
12	chr21:16531800-16532800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr21:16532000-16533000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr21:16532000-16533400	Enhancers	Monocytes-CD14+_RO01746	blood
15	chr21:16532200-16535000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr21:16532200-16536600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr21:16532600-16535600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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