Variant report

Variant	rs17024035
Chromosome Location	chr2:100968560-100968561
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:100935867..100940254-chr2:100962502..100969736,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000170500	Chromatin interaction

Extended variants
information (count: 123 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs10167159	1.00[ASN][1000 genomes]
rs10172841	0.93[GIH][hapmap]
rs10180570	0.88[ASN][1000 genomes]
rs10184899	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193535	1.00[CHB][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.88[ASN][1000 genomes]
rs10198495	1.00[ASN][1000 genomes]
rs10198682	1.00[ASN][1000 genomes]
rs10200480	1.00[ASN][1000 genomes]
rs10201098	1.00[ASN][1000 genomes]
rs10204833	1.00[ASN][1000 genomes]
rs10206374	1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10208900	1.00[ASN][1000 genomes]
rs10208911	1.00[ASN][1000 genomes]
rs10209186	1.00[ASN][1000 genomes]
rs1057056	1.00[GIH][hapmap]
rs1107429	1.00[CHB][hapmap];1.00[JPT][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]
rs1124009	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs13391930	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13396147	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13400841	0.96[GIH][hapmap]
rs13404823	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407408	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407648	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13407891	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13410582	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13419808	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13420942	1.00[ASN][1000 genomes]
rs1347721	1.00[CHB][hapmap];0.88[ASN][1000 genomes]
rs1370627	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[ASN][1000 genomes]
rs1437970	1.00[ASN][1000 genomes]
rs1437972	0.93[GIH][hapmap]
rs17023985	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17024129	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024133	1.00[CHB][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap]
rs17024136	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024144	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17024209	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs1898571	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1898574	1.00[ASN][1000 genomes]
rs2309793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2309801	0.96[GIH][hapmap]
rs3748936	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs3791358	0.90[GIH][hapmap]
rs4149509	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs4149514	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4149515	1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap]
rs4850932	0.96[GIH][hapmap]
rs55640826	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs55843950	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56051859	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56118658	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs56342384	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56656536	0.88[ASN][1000 genomes]
rs58876304	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60131548	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60609848	0.88[ASN][1000 genomes]
rs60898093	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61321970	1.00[ASN][1000 genomes]
rs6542931	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542932	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542939	1.00[ASN][1000 genomes]
rs6542941	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6542946	0.93[GIH][hapmap]
rs6708942	0.88[ASN][1000 genomes]
rs6713862	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6714109	1.00[ASN][1000 genomes]
rs6716009	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6716367	0.88[ASN][1000 genomes]
rs6724695	1.00[CHB][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6725672	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6728575	0.93[GIH][hapmap]
rs6732285	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6739576	1.00[ASN][1000 genomes]
rs6740098	1.00[ASN][1000 genomes]
rs6750866	0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6754379	1.00[ASN][1000 genomes]
rs6754869	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6755395	1.00[ASN][1000 genomes]
rs6757774	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758156	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758161	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6758515	0.88[ASN][1000 genomes]
rs6758622	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6761561	0.88[ASN][1000 genomes]
rs72960172	1.00[ASN][1000 genomes]
rs72960184	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72960186	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72960202	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73966107	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73966108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73968412	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73968415	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73968817	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7556717	1.00[ASN][1000 genomes]
rs7557137	1.00[ASN][1000 genomes]
rs7559939	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7559946	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562461	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562479	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562486	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7562615	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7564178	0.88[ASN][1000 genomes]
rs7571659	0.93[GIH][hapmap]
rs7572119	0.88[ASN][1000 genomes]
rs7574684	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7575422	1.00[GIH][hapmap];1.00[TSI][hapmap]
rs7576749	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7582096	0.96[GIH][hapmap]
rs7582546	1.00[CHB][hapmap];1.00[EUR][1000 genomes]
rs7585713	0.96[GIH][hapmap]
rs7585898	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7587333	0.88[ASN][1000 genomes]
rs7597631	1.00[ASN][1000 genomes]
rs7597722	1.00[ASN][1000 genomes]
rs7598205	0.93[GIH][hapmap]
rs7606723	1.00[ASN][1000 genomes]
rs876439	0.93[GIH][hapmap]
rs9308834	0.88[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	nsv1007777	chr2:100816913-101308914	Active TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
2	nsv535844	chr2:100816913-101308914	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
3	nsv834311	chr2:100816917-100990036	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	nsv582531	chr2:100908508-101207639	Bivalent Enhancer Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
5	esv2754449	chr2:100966963-100969067	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs17024035	EGR4	trans	brain	seeQTL
rs17024035	PTGS2	trans	brain	seeQTL
rs17024035	ARC	trans	brain	seeQTL
rs17024035	DUSP2	trans	brain	seeQTL
rs17024035	FOSB	trans	brain	seeQTL
rs17024035	EGR2	trans	brain	seeQTL
rs17024035	NPAS4	trans	brain	seeQTL

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:100966800-100968600	Enhancers	Placenta	Placenta
2	chr2:100968200-100968600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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