Variant report

Variant	rs1542271
Chromosome Location	chr2:46694024-46694025
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:46691531..46694095-chr2:46695293..46698690,3	K562	blood:
2	chr2:46693043..46695866-chr2:46768148..46769721,2	MCF-7	breast:
3	chr2:46688831..46694095-chr2:46695879..46699021,6	K562	blood:
4	chr2:46683036..46684677-chr2:46693619..46695195,2	K562	blood:
5	chr2:46693283..46695227-chr2:46712341..46714395,2	K562	blood:
6	chr2:46693342..46696123-chr5:77522105..77524620,2	K562	blood:

Variant related genes	Relation type
ENSG00000119729	Chromatin interaction
ENSG00000250565	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs11125077	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12473626	0.92[CEU][hapmap];0.83[JPT][hapmap]
rs12619420	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs13009087	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13017856	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13018019	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13018477	0.96[CEU][hapmap];0.82[CHB][hapmap];0.94[JPT][hapmap];0.82[YRI][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13025174	1.00[CEU][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13025967	0.83[EUR][1000 genomes]
rs13032473	0.89[ASW][hapmap];1.00[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.81[MKK][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13033917	1.00[CEU][hapmap];0.82[CHB][hapmap];0.88[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1530625	0.92[CEU][hapmap];0.81[CHD][hapmap];0.82[EUR][1000 genomes]
rs1530627	1.00[CEU][hapmap];0.84[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1530628	0.84[CEU][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1597041	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1823561	0.96[ASN][1000 genomes]
rs1868080	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1868096	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2053765	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2084345	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2121697	0.95[CEU][hapmap];0.81[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2121700	0.88[CEU][hapmap]
rs2197698	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2276555	0.92[CEU][hapmap];0.80[MEX][hapmap]
rs3814047	1.00[CEU][hapmap];0.81[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3814048	0.92[EUR][1000 genomes]
rs3863000	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4366955	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4396767	0.83[CEU][hapmap]
rs4456747	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4953377	0.82[EUR][1000 genomes]
rs4953381	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4953384	0.92[EUR][1000 genomes]
rs4953385	0.89[ASW][hapmap];1.00[CEU][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.86[LWK][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4953389	0.92[CEU][hapmap];0.82[JPT][hapmap];0.82[YRI][hapmap]
rs6544894	0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6715279	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6726089	0.82[TSI][hapmap]
rs6728611	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6728847	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6737959	1.00[CEU][hapmap];0.95[CHD][hapmap];0.84[LWK][hapmap];0.80[MEX][hapmap];0.89[TSI][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7556828	0.80[CEU][hapmap]
rs7557998	0.84[ASW][hapmap];0.84[CEU][hapmap];0.83[CHD][hapmap];0.83[JPT][hapmap];0.89[LWK][hapmap]
rs7559484	0.92[CEU][hapmap];0.83[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.86[EUR][1000 genomes]
rs7562332	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7565770	0.84[CEU][hapmap];0.95[CHD][hapmap];0.84[JPT][hapmap];0.80[MEX][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7565850	0.86[EUR][1000 genomes]
rs7571742	0.92[CEU][hapmap];0.86[CHD][hapmap];0.80[MEX][hapmap];0.84[TSI][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7588586	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7588938	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap];0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7598507	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7598584	0.92[CEU][hapmap];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7598712	0.80[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012446	chr2:45921682-46737036	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	esv2757795	chr2:46532812-46874151	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	esv2759046	chr2:46532812-46874151	Active TSS Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
4	esv34650	chr2:46605659-46818992	Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
5	esv2756919	chr2:46614235-46756431	Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
6	nsv437435	chr2:46636967-46763587	Active TSS Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
7	esv34937	chr2:46651624-46818586	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
8	nsv9702	chr2:46668106-46745740	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
9	nsv817828	chr2:46670146-46739157	Weak transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
10	nsv1014425	chr2:46670179-47033417	Enhancers Strong transcription Flanking Active TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
11	nsv535678	chr2:46670179-47033417	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
12	nsv873996	chr2:46670941-47065227	Strong transcription Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
13	nsv519216	chr2:46683683-46723219	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1542271	ATP6V1E2	cis	multi-tissue	Pritchard
rs1542271	CRIPT	cis	lymphoblastoid	seeQTL
rs1542271	CRIPT	cis	parietal	SCAN
rs1542271	CRIPT	cis	multi-tissue	Pritchard
rs1542271	CRIPT	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:46686400-46704400	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr2:46689000-46696800	Weak transcription	K562	blood
3	chr2:46689200-46696600	Weak transcription	Fetal Thymus	thymus
4	chr2:46689200-46698600	Weak transcription	Hela-S3	cervix
5	chr2:46689200-46704800	Weak transcription	Placenta	Placenta
6	chr2:46689200-46714800	Weak transcription	Right Atrium	heart
7	chr2:46689800-46697000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr2:46689800-46697400	Weak transcription	Primary B cells from peripheral blood	blood
9	chr2:46690000-46696800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr2:46691600-46696800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:46691800-46695800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:46691800-46696400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
13	chr2:46691800-46696400	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr2:46691800-46696400	Weak transcription	Monocytes-CD14+_RO01746	blood
15	chr2:46691800-46696800	Weak transcription	Adipose Nuclei	Adipose
16	chr2:46692000-46696800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr2:46692000-46702600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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