Variant report

Variant	rs2953518
Chromosome Location	chr8:87330873-87330874
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87232045..87233654-chr8:87330272..87332535,2	MCF-7	breast:
2	chr8:87329883..87331903-chr8:87367165..87369926,2	MCF-7	breast:
3	chr8:87329069..87335338-chr8:87352769..87359177,10	MCF-7	breast:
4	chr8:87329552..87331858-chr8:87353480..87355927,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123124	Chromatin interaction
ENSG00000254231	Chromatin interaction

Extended variants
information (count: 133 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:112)

rs_ID	r²[population]
rs10089169	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10089253	0.85[EUR][1000 genomes]
rs10089317	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10090898	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs10092168	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10093867	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10097546	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10097866	0.85[EUR][1000 genomes]
rs10098365	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs10100368	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap]
rs10100698	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10106855	1.00[ASN][1000 genomes]
rs10107571	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs10108586	0.85[EUR][1000 genomes]
rs10109032	0.85[ASN][1000 genomes]
rs10109677	0.88[EUR][1000 genomes]
rs10113158	0.97[ASN][1000 genomes]
rs10504823	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10956820	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10956821	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10956822	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11774253	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11776698	0.85[EUR][1000 genomes]
rs11781993	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11783382	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs11984519	0.81[EUR][1000 genomes]
rs11986423	0.92[GIH][hapmap];0.83[TSI][hapmap]
rs11994508	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs11997927	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs12155979	0.90[EUR][1000 genomes]
rs12155981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs12156004	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12216783	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12335013	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12677915	0.84[CEU][hapmap]
rs13265266	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1595207	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs17681534	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17681826	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2118070	0.82[CEU][hapmap];0.88[EUR][1000 genomes]
rs28384362	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28397606	0.81[EUR][1000 genomes]
rs28416254	0.81[EUR][1000 genomes]
rs28433311	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28445847	0.97[ASN][1000 genomes]
rs28504479	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28680173	0.84[EUR][1000 genomes]
rs28715255	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28783474	0.97[ASN][1000 genomes]
rs2917553	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917559	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2917561	0.88[EUR][1000 genomes]
rs2953507	0.97[ASN][1000 genomes]
rs2953508	0.97[ASN][1000 genomes]
rs2953512	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953514	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953515	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953519	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2953520	0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2953521	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs2953523	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs2953524	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2953526	0.88[EUR][1000 genomes]
rs2954348	0.91[CEU][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap]
rs2976170	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976173	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976174	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976175	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976176	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976180	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976192	0.90[ASN][1000 genomes]
rs2976194	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2976195	0.93[ASN][1000 genomes]
rs2976196	0.93[ASN][1000 genomes]
rs2976199	0.93[ASN][1000 genomes]
rs2976200	0.84[CEU][hapmap];0.81[GIH][hapmap];0.83[TSI][hapmap];0.83[YRI][hapmap]
rs2976202	0.97[ASN][1000 genomes]
rs2976203	0.83[EUR][1000 genomes]
rs3087641	1.00[CHD][hapmap];0.96[GIH][hapmap];0.81[EUR][1000 genomes]
rs4370511	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4440616	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs4628240	0.88[EUR][1000 genomes]
rs4633041	0.91[CEU][hapmap];0.88[EUR][1000 genomes]
rs55671538	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55871514	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58837061	0.85[EUR][1000 genomes]
rs6471266	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs6471284	0.97[ASN][1000 genomes]
rs6471295	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6471317	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6980476	1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap]
rs6993497	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6993612	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7015772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7018083	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs73262925	0.97[ASN][1000 genomes]
rs73262927	0.97[ASN][1000 genomes]
rs73688817	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73688823	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73688824	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73688827	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7815489	0.97[ASN][1000 genomes]
rs7818436	0.81[EUR][1000 genomes]
rs7837581	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7837618	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7839096	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7843272	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7843399	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7846468	0.97[ASN][1000 genomes]
rs9297913	0.81[EUR][1000 genomes]
rs9656823	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9656824	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529563	chr8:86467090-87381984	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
2	nsv932023	chr8:86845979-87490694	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases
3	nsv891147	chr8:86886950-87333968	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
4	nsv429926	chr8:87161695-87429872	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv1020485	chr8:87167184-87330873	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv1023114	chr8:87167184-87335197	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv1033960	chr8:87167790-87334194	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	nsv1016050	chr8:87167790-87335197	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
9	nsv1023772	chr8:87177368-87334194	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
10	nsv1031874	chr8:87177368-87335197	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	nsv1030401	chr8:87177368-87337260	Enhancers Bivalent Enhancer Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
12	esv2761445	chr8:87185470-87335197	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
13	esv3349873	chr8:87185763-87603726	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
14	nsv519507	chr8:87187195-87333968	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	nsv1020459	chr8:87200116-87330912	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
16	nsv539660	chr8:87200116-87330912	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
17	esv3360246	chr8:87200232-87419244	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
18	nsv611708	chr8:87205885-87333968	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
19	nsv1021125	chr8:87208343-87331289	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
20	nsv539661	chr8:87208343-87331289	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
21	nsv1017535	chr8:87261702-87367934	Flanking Active TSS Weak transcription Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2953518	DECR1	cis	parietal	SCAN
rs2953518	MMP16	cis	parietal	SCAN
rs2953518	CPNE3	cis	cerebellum	SCAN
rs2953518	CPNE3	cis	parietal	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87318400-87333200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr8:87328400-87332200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
3	chr8:87328400-87332400	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr8:87328600-87332400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr8:87328600-87333800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr8:87328600-87333800	Weak transcription	Primary T helper cells PMA-I stimulated	--
7	chr8:87329200-87331000	Weak transcription	Esophagus	oesophagus
8	chr8:87329600-87332200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr8:87330000-87331000	Weak transcription	Liver	Liver
10	chr8:87330800-87334800	Enhancers	Fetal Lung	lung

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