Variant report

Variant	rs1376444
Chromosome Location	chr2:100141028-100141029
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	chr2:100124800..100126924-chr2:100140530..100142431,2	MCF-7	breast:

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10173883	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10175852	0.86[EUR][1000 genomes]
rs10176205	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10179435	0.85[EUR][1000 genomes]
rs10179697	0.88[CEU][hapmap];1.00[CHB][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10180138	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10180688	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs10186223	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10191001	1.00[CHB][hapmap]
rs10207435	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10210257	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10210346	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs10496337	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs11123784	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs12623835	0.86[CEU][hapmap]
rs13028722	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs13394927	0.85[MEX][hapmap]
rs13401163	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13402784	0.85[MEX][hapmap]
rs13405400	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13409359	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.85[EUR][1000 genomes]
rs13415713	0.88[CEU][hapmap];1.00[CHB][hapmap];0.87[EUR][1000 genomes]
rs13416265	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13419448	1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs13420087	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13426758	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13427424	0.83[EUR][1000 genomes]
rs13429185	0.88[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes]
rs13429806	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs13430962	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13431410	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs13432046	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs1882598	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs1901284	0.80[ASN][1000 genomes]
rs2309577	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs28369929	0.82[MEX][hapmap]
rs28369949	0.83[EUR][1000 genomes]
rs28382945	0.83[EUR][1000 genomes]
rs28382947	0.83[EUR][1000 genomes]
rs28745279	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs3087399	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs3792151	0.85[MEX][hapmap]
rs3828162	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap]
rs6712137	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs6726711	1.00[CEU][hapmap];1.00[CHB][hapmap]
rs6746402	0.80[ASN][1000 genomes]
rs72817011	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7569805	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs7579143	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap]
rs7582085	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7582133	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs7585532	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7599384	0.88[CEU][hapmap];1.00[CHB][hapmap]
rs9308819	0.88[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.83[EUR][1000 genomes]
rs9308821	0.88[CEU][hapmap];1.00[CHB][hapmap];0.85[EUR][1000 genomes]
rs9308822	0.88[CEU][hapmap];1.00[CHB][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9308823	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv431424	chr2:99652682-100494682	Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
2	nsv962113	chr2:100022168-100317461	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1376444	LIPT1	cis	cerebellum	SCAN
rs1376444	LYG1	cis	parietal	SCAN
rs1376444	ARID5A	cis	parietal	SCAN
rs1376444	TSGA10	cis	cerebellum	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100140600-100141200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr2:100140600-100141400	Enhancers	Fetal Heart	heart
3	chr2:100140800-100141200	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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