Variant report

Variant	rs2838673
Chromosome Location	chr21:46180309-46180310
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr21:46173002..46174537-chr21:46178694..46181185,2	MCF-7	breast:
2	chr21:46179049..46181876-chr21:46183341..46186313,2	K562	blood:
3	chr21:46179049..46181876-chr21:46183341..46186313,3	K562	blood:
4	chr21:46175791..46179741-chr21:46180006..46182976,4	K562	blood:

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1071792	0.80[EUR][1000 genomes]
rs1109280	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs1347324	0.83[EUR][1000 genomes]
rs1821431	0.84[EUR][1000 genomes]
rs2294157	0.84[EUR][1000 genomes]
rs2329899	0.84[EUR][1000 genomes]
rs2329900	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs2838674	1.00[ASN][1000 genomes]
rs2838675	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2838678	0.84[EUR][1000 genomes]
rs2838686	0.85[CEU][hapmap];0.84[EUR][1000 genomes]
rs3788136	0.85[EUR][1000 genomes]
rs4239838	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs4818973	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4818974	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4818975	0.80[CEU][hapmap];0.84[EUR][1000 genomes]
rs55659309	1.00[ASN][1000 genomes]
rs733161	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs760430	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs760431	0.80[CEU][hapmap]
rs8103	0.84[CEU][hapmap];0.85[EUR][1000 genomes]
rs8128992	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs8133039	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs885655	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885656	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs885657	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916258	chr21:45995986-46624705	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
2	nsv913956	chr21:46096964-46279505	Enhancers Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv1062245	chr21:46096964-46332587	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv544478	chr21:46096964-46332587	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2838673	UBE2G2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr21:46168000-46185800	Weak transcription	Right Atrium	heart
2	chr21:46171400-46183400	Weak transcription	Gastric	stomach
3	chr21:46173000-46180800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr21:46179000-46183400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr21:46179200-46180400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr21:46179600-46184600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr21:46179800-46182000	Enhancers	H1 Cell Line	embryonic stem cell
8	chr21:46180000-46180600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr21:46180000-46180800	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr21:46180000-46181800	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr21:46180200-46180400	Enhancers	iPS-20b Cell Line	embryonic stem cell
12	chr21:46180200-46181600	Enhancers	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links