Variant report

Variant	rs9298497
Chromosome Location	chr8:54936282-54936283
allele	G/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	FOS	chr8:54936174-54936297	MCF10A-Er-Src	breast:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246
2	CUX1	chr8:54935973-54936302	K562	blood:	n/a	n/a
3	JUN	chr8:54934606-54936862	K562	blood:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
4	POLR2A	chr8:54933772-54936292	K562	blood:	n/a	n/a
5	RCOR1	chr8:54933955-54936293	K562	blood:	n/a	n/a
6	JUND	chr8:54935801-54936455	HCT-116	colon:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
7	POLR2A	chr8:54935723-54936324	H1-hESC	embryonic stem cell:	n/a	n/a
8	FOS	chr8:54936079-54936368	MCF10A-Er-Src	breast:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
9	POLR2A	chr8:54935467-54936285	K562	blood:	n/a	n/a
10	EP300	chr8:54936094-54936311	GM12878	blood:	n/a	chr8:54936237-54936246
11	JUN	chr8:54936046-54936333	K562	blood:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
12	JUND	chr8:54935669-54936420	K562	blood:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
13	POLR2A	chr8:54934174-54936297	K562	blood:	n/a	n/a
14	FOSL2	chr8:54936037-54936345	MCF-7	breast:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
15	FOS	chr8:54936057-54936398	MCF10A-Er-Src	breast:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
16	BATF	chr8:54936055-54936312	GM12878	blood:	n/a	chr8:54936234-54936244
17	ARID3A	chr8:54936016-54936352	K562	blood:	n/a	n/a
18	FOSL1	chr8:54935876-54936509	HCT-116	colon:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
19	JUND	chr8:54935893-54936471	HCT-116	colon:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246 chr8:54936129-54936136
20	FOS	chr8:54936146-54936369	MCF10A-Er-Src	breast:	n/a	chr8:54936237-54936244 chr8:54936235-54936247 chr8:54936237-54936246

No.	Distal block	Cell Line	Cell type
1	chr8:54932312..54937718-chr8:55045869..55049283,5	MCF-7	breast:
2	chr8:54929833..54936668-chr8:55008421..55016367,12	K562	blood:
3	chr8:54931365..54936825-chr8:55013053..55016452,9	MCF-7	breast:
4	chr8:54935168..54936704-chr8:55014471..55015988,2	K562	blood:
5	chr8:54933199..54936694-chr8:55047814..55049965,3	K562	blood:
6	chr8:54933199..54936650-chr8:55046856..55051256,7	K562	blood:
7	chr8:54754942..54758152-chr8:54933404..54936388,3	K562	blood:

Variant related genes	Relation type
TCEA1	TF binding region
ENSG00000120992	Chromatin interaction
ENSG00000047249	Chromatin interaction
ENSG00000137547	Chromatin interaction

Extended variants
information (count: 79 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10101097	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10113246	0.94[ASN][1000 genomes]
rs1039926	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs10504161	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs1050523	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10958396	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.80[EUR][1000 genomes]
rs10958397	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs11783652	0.82[CHB][hapmap]
rs11986577	1.00[CHB][hapmap];0.97[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11991952	0.87[CHB][hapmap];0.85[GIH][hapmap];0.80[JPT][hapmap]
rs11993367	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11993959	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs11994629	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11996666	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11997954	0.97[ASN][1000 genomes]
rs12056381	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12114043	0.81[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs12674671	0.97[ASN][1000 genomes]
rs12676510	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12677696	0.87[AMR][1000 genomes]
rs12679542	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs16919699	0.80[CHB][hapmap]
rs16919782	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs16919784	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs1828835	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2037068	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2271567	0.91[CEU][hapmap];0.87[CHB][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.82[MKK][hapmap];0.84[TSI][hapmap];0.92[YRI][hapmap]
rs2292590	0.91[CEU][hapmap];0.87[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap]
rs2375697	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28494618	0.96[ASN][1000 genomes]
rs4440612	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4506187	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4515510	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4737457	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4737479	0.83[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];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4737485	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4737486	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4737487	1.00[CHB][hapmap];0.94[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.88[TSI][hapmap]
rs4737488	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs4738519	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4738544	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4738556	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4738586	0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57872947	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58387069	0.83[AFR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs58419852	0.83[ASN][1000 genomes]
rs58929175	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs58948369	0.80[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs59882028	0.83[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs60183530	0.83[ASN][1000 genomes]
rs61319412	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6473900	0.97[ASN][1000 genomes]
rs6473909	0.80[ASN][1000 genomes]
rs6473911	0.87[CHB][hapmap];0.85[JPT][hapmap]
rs6473914	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs6473915	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs6983694	0.83[ASN][1000 genomes]
rs7009781	0.96[ASN][1000 genomes]
rs7011379	0.82[ASN][1000 genomes]
rs7012031	0.87[CHB][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs72614663	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs72614664	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72614665	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72614666	0.83[ASN][1000 genomes]
rs72614667	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs72614668	0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7463083	1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.88[TSI][hapmap]
rs7463261	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7464767	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.88[TSI][hapmap];0.96[ASN][1000 genomes]
rs7815216	0.95[ASN][1000 genomes]
rs7842911	0.93[CHB][hapmap];0.81[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.84[TSI][hapmap]
rs952194	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap]
rs9643823	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9643824	0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023983	chr8:54790309-55145770	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv539623	chr8:54790309-55145770	Bivalent Enhancer Genic enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	esv2758160	chr8:54832990-55016965	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	esv2759617	chr8:54832990-55016965	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
5	nsv427821	chr8:54832990-55016965	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs9298497	MRPL15	cis	lymphoblastoid	seeQTL
rs9298497	MRPL15	cis	cerebellum	SCAN
rs9298497	TCEA1	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:54933400-54936400	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr8:54935400-54962800	Weak transcription	HSMMtube	muscle
3	chr8:54935600-54946000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr8:54935600-54954600	Weak transcription	HSMM	muscle
5	chr8:54935600-54955600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr8:54935600-54956600	Weak transcription	Pancreas	Pancrea
7	chr8:54935600-54956600	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr8:54935600-54956600	Weak transcription	HUVEC	blood vessel
9	chr8:54935600-54963000	Weak transcription	Thymus	Thymus
10	chr8:54935800-54936400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr8:54935800-54943400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr8:54936000-54943400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr8:54936000-54945200	Weak transcription	Placenta	Placenta
14	chr8:54936200-54936400	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr8:54936200-54936400	Active TSS	K562	blood
16	chr8:54936200-54938000	Weak transcription	NHEK	skin
17	chr8:54936200-54943800	Weak transcription	A549	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links