Variant report

Variant	rs2999563
Chromosome Location	chr1:152046995-152046996
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:152003216..152005599-chr1:152046745..152048519,2	MCF-7	breast:
2	chr1:152042308..152047029-chr1:152081777..152083465,4	MCF-7	breast:
3	chr1:152043286..152045269-chr1:152045806..152047940,2	MCF-7	breast:
4	chr1:151964883..151966894-chr1:152045649..152048031,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000197747	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10788821	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1131471	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1131473	0.90[JPT][hapmap]
rs11588437	0.80[CHB][hapmap];0.90[JPT][hapmap]
rs12033735	0.96[CEU][hapmap];0.89[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1496036	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1496041	0.90[JPT][hapmap]
rs2069258	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2496253	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2935208	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3001974	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3001978	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3007680	0.84[JPT][hapmap]
rs3122305	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3124316	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs4579760	0.92[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4845419	0.96[CEU][hapmap];0.85[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4845420	0.96[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6700989	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs72696919	0.80[EUR][1000 genomes]
rs924087	0.81[CEU][hapmap];0.95[JPT][hapmap];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007097	chr1:151832796-152227977	Strong transcription Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
2	nsv1012327	chr1:151835544-152200890	Enhancers Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
3	nsv535159	chr1:151835544-152200890	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	196 gene(s)	inside rSNPs	diseases
4	nsv547853	chr1:152008671-152236760	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
5	nsv535160	chr1:152031280-152050179	Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2999563	THEM4	Cis_1M	lymphoblastoid	RTeQTL
rs2999563	S100A10	Cis_1M	lymphoblastoid	RTeQTL
rs2999563	S100A10	cis	multi-tissue	Pritchard

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
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