Variant report

Variant	rs7565275
Chromosome Location	chr2:234229320-234229321
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ATG16L1-3	chr2:234229276-234229370	NONHSAT077476

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1000548	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.84[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10803619	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11679064	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs11682236	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11682898	1.00[CHB][hapmap]
rs11694406	0.86[JPT][hapmap]
rs11890330	1.00[CEU][hapmap];0.81[ASN][1000 genomes]
rs11890449	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2289476	1.00[CHB][hapmap]
rs2304775	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3792099	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3792101	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3828307	0.84[ASW][hapmap];0.82[CEU][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.87[TSI][hapmap];0.92[YRI][hapmap]
rs3828308	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs55754152	0.81[ASN][1000 genomes]
rs55895356	0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56242862	0.81[ASN][1000 genomes]
rs59303693	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6719241	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6748547	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap]
rs6753242	0.86[JPT][hapmap]
rs72976324	0.81[ASN][1000 genomes]
rs72976366	0.81[ASN][1000 genomes]
rs72978306	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978311	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978313	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978315	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72978317	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7564805	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7578402	0.81[ASN][1000 genomes]
rs7583380	1.00[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7585217	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7594365	0.81[ASN][1000 genomes]
rs7594781	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584699	chr2:234182240-234255547	Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
2	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234222200-234230200	Weak transcription	GM12878-XiMat	blood
2	chr2:234222600-234229800	Weak transcription	Primary B cells from cord blood	blood
3	chr2:234223600-234245400	Weak transcription	Pancreas	Pancrea
4	chr2:234227600-234229800	Weak transcription	Primary B cells from peripheral blood	blood
5	chr2:234228400-234240000	Weak transcription	Fetal Intestine Small	intestine
6	chr2:234228600-234231400	Enhancers	Fetal Brain Male	brain
7	chr2:234229200-234229400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:234229200-234229400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr2:234229200-234229600	Bivalent Enhancer	HepG2	liver

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