Variant report

Variant	rs1574242
Chromosome Location	chr7:48046714-48046715
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr7:48046701-48046768	MCF-7	breast:	n/a	n/a
2	ZNF143	chr7:48046650-48046795	H1-hESC	embryonic stem cell:	n/a	n/a
3	MYC	chr7:48046678-48046734	MCF-7	breast:	n/a	n/a
4	ZNF143	chr7:48046686-48046873	GM12878	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:48044680..48047190-chr7:48067195..48070779,3	K562	blood:

Variant related genes	Relation type
SUN3	TF binding region
ENSG00000164744	Chromatin interaction

Extended variants
information (count: 70 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10225968	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.98[TSI][hapmap]
rs10247913	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs10253220	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[EUR][1000 genomes]
rs10253238	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10256256	0.84[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10261930	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10951937	0.80[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951938	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10951940	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951941	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10951942	0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs11761275	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11762077	0.96[CEU][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11764799	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11766144	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11766891	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11767002	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.95[MEX][hapmap];0.84[MKK][hapmap];0.98[TSI][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11768277	1.00[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11772387	1.00[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11772633	0.82[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11773348	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12535580	0.96[CEU][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12537979	1.00[CEU][hapmap];0.94[JPT][hapmap]
rs12702405	0.83[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12702406	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1318327	0.96[CEU][hapmap];0.89[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13230023	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1915960	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1915962	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1915965	0.92[CEU][hapmap];0.98[GIH][hapmap];0.89[JPT][hapmap];0.91[TSI][hapmap]
rs1915966	1.00[CEU][hapmap];0.81[CHB][hapmap];0.94[JPT][hapmap];0.99[EUR][1000 genomes]
rs1915967	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1915968	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1915971	0.96[CEU][hapmap];0.90[JPT][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1915972	0.96[CEU][hapmap];0.89[JPT][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2037482	0.96[CEU][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2140113	0.96[CEU][hapmap];0.82[CHB][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.95[TSI][hapmap]
rs2348666	0.89[ASW][hapmap];0.96[CEU][hapmap];0.95[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.90[MEX][hapmap];0.83[MKK][hapmap];0.93[TSI][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2348667	0.95[CEU][hapmap];0.89[JPT][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2348669	0.96[CEU][hapmap];0.82[CHB][hapmap];0.90[JPT][hapmap];0.96[YRI][hapmap]
rs2348670	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2708883	0.85[TSI][hapmap]
rs2708909	0.83[TSI][hapmap]
rs2881991	0.92[CEU][hapmap];0.90[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[TSI][hapmap];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2881992	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4332046	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4618593	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6978838	0.96[CEU][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6979699	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7357251	0.96[CEU][hapmap];0.90[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7357327	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7456745	0.96[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7779252	1.00[ASW][hapmap];0.96[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.95[MKK][hapmap];0.98[TSI][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7791084	0.92[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791572	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7791823	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7800590	0.83[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs7807611	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807612	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807654	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7807750	0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7808462	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9690905	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1026223	chr7:47560728-48243287	Genic enhancers Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv869585	chr7:47765428-48151324	Flanking Active TSS Enhancers Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv532120	chr7:47882757-48195869	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
4	nsv470221	chr7:47917495-48354363	Strong transcription Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv464442	chr7:47917495-48354820	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Bivalent/Poised TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv606893	chr7:47917495-48354820	Flanking Active TSS Strong transcription Genic enhancers Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv888004	chr7:48028771-48120717	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1574242	PKD1L1	cis	parietal	SCAN
rs1574242	C7orf57	cis	Esophagus Mucosa	GTEx
rs1574242	UPP1	cis	Muscle Skeletal	GTEx
rs1574242	PKD1L1	cis	cerebellum	SCAN
rs1574242	UPP1	cis	cerebellum	SCAN
rs1574242	ABCA13	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:48031800-48050200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr7:48044000-48047000	Enhancers	GM12878-XiMat	blood
3	chr7:48045000-48047000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr7:48045800-48047200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr7:48045800-48047200	Enhancers	Fetal Lung	lung
6	chr7:48046400-48046800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr7:48046600-48046800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr7:48046600-48047000	Enhancers	Fetal Intestine Small	intestine

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links