Variant report

Variant	rs259002
Chromosome Location	chr7:110552797-110552798
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:110545807..110549093-chr7:110551950..110553990,3	K562	blood:
2	chr7:110551799..110553652-chr7:110557425..110559559,2	K562	blood:

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs1008413	0.82[EUR][1000 genomes]
rs10225614	1.00[CEU][hapmap];0.88[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs10246351	0.82[EUR][1000 genomes]
rs10260255	0.81[EUR][1000 genomes]
rs10464508	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10464637	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs115825	0.88[CHB][hapmap];0.97[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs115826	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12534893	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12535802	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12537585	0.83[CEU][hapmap]
rs12540013	0.93[EUR][1000 genomes]
rs12540274	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12672824	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs166308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs174074	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17438711	1.00[CEU][hapmap];0.92[JPT][hapmap];0.92[EUR][1000 genomes]
rs17527832	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17528429	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17528930	1.00[CEU][hapmap];0.88[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2041531	1.00[CEU][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2109863	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs2191926	1.00[CEU][hapmap];0.84[CHD][hapmap];0.88[GIH][hapmap];0.93[JPT][hapmap];0.91[MEX][hapmap];0.98[TSI][hapmap];0.92[EUR][1000 genomes]
rs2396300	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs258988	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap]
rs258989	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258990	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258991	1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs258992	1.00[CEU][hapmap]
rs258994	1.00[CEU][hapmap]
rs258995	1.00[CEU][hapmap]
rs258996	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.97[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap]
rs258997	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258998	0.81[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.83[MEX][hapmap];0.89[TSI][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs258999	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs259000	0.96[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259003	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs259004	0.92[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.93[CHD][hapmap];0.94[GIH][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs259006	0.92[ASW][hapmap];1.00[CEU][hapmap];0.94[GIH][hapmap];0.86[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs259008	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs259009	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs259011	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs259012	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];1.00[TSI][hapmap]
rs259013	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs259014	0.84[EUR][1000 genomes]
rs259015	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs259017	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs259018	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs259020	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs259021	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs259022	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4141112	0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4727753	1.00[CEU][hapmap];0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.93[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4730467	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4730468	0.83[CEU][hapmap];0.84[EUR][1000 genomes]
rs4730470	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs4730472	0.83[CEU][hapmap];0.83[MEX][hapmap];0.81[EUR][1000 genomes]
rs55693011	0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs56148096	0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56160040	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56277540	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56379568	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs56907799	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs57167163	0.88[ASN][1000 genomes]
rs57238777	0.90[EUR][1000 genomes]
rs58495202	0.91[EUR][1000 genomes]
rs58585976	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs59086405	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs60581416	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs60807734	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6466365	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6466366	0.83[CEU][hapmap];0.85[EUR][1000 genomes]
rs6466368	1.00[CEU][hapmap];0.89[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs6466370	1.00[CEU][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes]
rs66596422	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67679818	0.92[EUR][1000 genomes]
rs67759016	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs67798998	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6955060	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6960818	0.93[EUR][1000 genomes]
rs6972608	1.00[CEU][hapmap];0.86[JPT][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6978507	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs725272	1.00[CEU][hapmap];0.89[GIH][hapmap];0.86[JPT][hapmap];0.96[MEX][hapmap];0.98[TSI][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs73435146	0.91[EUR][1000 genomes]
rs758952	1.00[CHB][hapmap];0.83[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs758954	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7782551	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7795011	0.83[CEU][hapmap];0.81[EUR][1000 genomes]
rs7796806	1.00[CEU][hapmap];0.93[JPT][hapmap];0.95[MEX][hapmap];0.95[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7809411	0.88[CHB][hapmap];0.90[CHD][hapmap];0.83[GIH][hapmap];0.86[JPT][hapmap]
rs799616	0.80[MEX][hapmap]
rs799623	0.83[ASW][hapmap];0.80[MEX][hapmap]
rs799624	0.83[ASW][hapmap];0.80[MEX][hapmap]
rs799625	0.83[ASW][hapmap]
rs876396	1.00[CEU][hapmap];0.92[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs917763	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9690080	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][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	nsv1023596	chr7:109984459-110708071	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Genic enhancers Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv539061	chr7:109984459-110708071	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
3	nsv608147	chr7:110292046-110617845	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv531434	chr7:110310931-110839892	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv888972	chr7:110470629-110635497	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
6	esv3506497	chr7:110484691-111091738	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	esv3506498	chr7:110484750-111091689	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv1019911	chr7:110505973-110570241	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
9	nsv888973	chr7:110509579-110699652	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
10	nsv888974	chr7:110516659-110660055	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
11	esv2758129	chr7:110523298-110787849	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
12	esv2759554	chr7:110523298-110787849	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
13	nsv1031546	chr7:110549137-110978256	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs259002	IMMP2L	Cis_1M	lymphoblastoid	RTeQTL
rs259002	IMMP2L	cis	lymphoblastoid	seeQTL
rs259002	IMMP2L	cis	multi-tissue	Pritchard

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:110550200-110562000	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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