Variant report

Variant	rs13020884
Chromosome Location	chr2:172901699-172901700
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:172900249..172901946-chr2:172954569..172956583,2	MCF-7	breast:
2	chr2:172900609..172903455-chr2:172958625..172961122,3	MCF-7	breast:
3	chr2:172900542..172905634-chr2:172946761..172951890,10	MCF-7	breast:

Variant related genes	Relation type
ENSG00000144355	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs1008151	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12052246	0.85[CEU][hapmap];0.91[MEX][hapmap];0.83[TSI][hapmap];0.80[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12987931	0.92[CHB][hapmap];1.00[CHD][hapmap];0.88[JPT][hapmap];0.81[YRI][hapmap];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12989560	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12991740	0.85[CEU][hapmap]
rs13015360	0.82[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1965160	0.92[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34054371	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34737109	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62183819	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433323	0.85[CEU][hapmap];0.87[MEX][hapmap];0.83[TSI][hapmap]
rs6718013	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs6730085	0.83[CHD][hapmap]
rs6737308	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs7584187	0.84[CHB][hapmap];0.84[CHD][hapmap]
rs7586556	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs788163	0.88[YRI][hapmap]
rs788166	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs788170	1.00[CEU][hapmap];0.92[YRI][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs788171	1.00[CEU][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.92[YRI][hapmap];0.83[AMR][1000 genomes];0.83[EUR][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	nsv875411	chr2:172693780-172942448	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
2	esv2830399	chr2:172781830-172952526	Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	nsv1012188	chr2:172855923-172928891	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	esv1798626	chr2:172900948-172909852	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13020884	MAP1D	cis	cerebellum	SCAN
rs13020884	SLC25A12	cis	parietal	SCAN
rs13020884	AC068039.4	cis	Adipose Subcutaneous	GTEx
rs13020884	MAP1D	cis	parietal	SCAN
rs13020884	SLC25A12	cis	cerebellum	SCAN
rs13020884	GORASP2	cis	cerebellum	SCAN
rs13020884	AC068039.4	cis	Muscle Skeletal	GTEx
rs13020884	AC068039.4	cis	Esophagus Mucosa	GTEx
rs13020884	AC068039.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172887400-172902800	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr2:172893600-172902000	Weak transcription	K562	blood
3	chr2:172897000-172902600	Weak transcription	Spleen	Spleen
4	chr2:172897800-172902600	Weak transcription	Psoas Muscle	Psoas
5	chr2:172901200-172907400	Weak transcription	Fetal Kidney	kidney
6	chr2:172901600-172903600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin

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