Variant report

Variant	rs2953524
Chromosome Location	chr8:87316379-87316380
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr8:87315946..87318767-chr8:87320826..87322918,2	MCF-7	breast:
2	chr8:87302798..87305553-chr8:87314921..87316646,2	MCF-7	breast:
3	chr8:87312932..87319525-chr8:87352143..87356441,7	MCF-7	breast:

Variant related genes	Relation type
ENSG00000123124	Chromatin interaction
ENSG00000254231	Chromatin interaction

Extended variants
information (count: 106 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:82)

rs_ID	r²[population]
rs10089169	0.91[CEU][hapmap]
rs10089317	0.84[EUR][1000 genomes]
rs10090898	1.00[CEU][hapmap]
rs10093867	0.83[EUR][1000 genomes]
rs10097546	0.83[EUR][1000 genomes]
rs10100698	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs10108632	0.84[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs10504823	0.84[EUR][1000 genomes]
rs10956820	0.91[CEU][hapmap]
rs10956822	0.91[CEU][hapmap]
rs11774253	0.91[CEU][hapmap]
rs11781993	0.83[EUR][1000 genomes]
rs11783382	0.91[CEU][hapmap]
rs11994508	0.91[CEU][hapmap]
rs11997927	0.90[CEU][hapmap]
rs12155981	0.91[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.95[TSI][hapmap]
rs12156004	0.85[EUR][1000 genomes]
rs12216783	0.84[EUR][1000 genomes]
rs12546256	0.83[EUR][1000 genomes]
rs12548143	0.83[EUR][1000 genomes]
rs12677915	0.92[CEU][hapmap];0.93[YRI][hapmap];0.84[EUR][1000 genomes]
rs13265266	0.83[EUR][1000 genomes]
rs13266677	0.84[EUR][1000 genomes]
rs13278499	0.84[EUR][1000 genomes]
rs1595207	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[GIH][hapmap];0.86[JPT][hapmap];0.98[LWK][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17681534	0.89[CEU][hapmap];0.84[EUR][1000 genomes]
rs17681826	0.91[CEU][hapmap]
rs2118070	0.91[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28433311	0.85[EUR][1000 genomes]
rs28504479	0.83[EUR][1000 genomes]
rs2917553	0.88[EUR][1000 genomes]
rs2917559	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2917561	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2953512	0.83[CEU][hapmap];0.81[GIH][hapmap];0.91[MEX][hapmap]
rs2953514	0.83[CEU][hapmap];0.83[YRI][hapmap]
rs2953515	0.83[CEU][hapmap];0.83[YRI][hapmap]
rs2953518	0.91[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs2953519	0.88[EUR][1000 genomes]
rs2953520	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2953521	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2953523	1.00[CEU][hapmap];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];0.98[ASN][1000 genomes]
rs2953525	0.92[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2953526	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2954348	0.83[CEU][hapmap];0.85[GIH][hapmap];0.91[MEX][hapmap];0.91[TSI][hapmap];0.85[EUR][1000 genomes]
rs2976170	0.88[EUR][1000 genomes]
rs2976173	0.88[EUR][1000 genomes]
rs2976174	0.87[EUR][1000 genomes]
rs2976175	0.88[EUR][1000 genomes]
rs2976176	0.90[CEU][hapmap];0.88[EUR][1000 genomes]
rs2976180	0.83[CEU][hapmap]
rs2976192	0.85[EUR][1000 genomes]
rs2976194	0.84[EUR][1000 genomes]
rs2976195	0.86[EUR][1000 genomes]
rs2976196	0.86[EUR][1000 genomes]
rs2976199	0.87[EUR][1000 genomes]
rs2976200	0.92[CEU][hapmap];0.81[GIH][hapmap];0.83[MKK][hapmap];0.83[TSI][hapmap];0.90[YRI][hapmap];0.83[EUR][1000 genomes]
rs2976203	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs3087641	0.88[GIH][hapmap]
rs4310185	0.81[AFR][1000 genomes];0.84[EUR][1000 genomes]
rs4327843	0.82[EUR][1000 genomes]
rs4413753	0.84[EUR][1000 genomes]
rs4440616	0.91[CEU][hapmap];0.88[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap]
rs4460347	0.82[EUR][1000 genomes]
rs4584127	0.83[EUR][1000 genomes]
rs4628240	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4633041	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55671538	0.85[EUR][1000 genomes]
rs6471266	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6471295	0.83[EUR][1000 genomes]
rs7015335	0.83[EUR][1000 genomes]
rs7015772	0.91[CEU][hapmap]
rs73688817	0.84[EUR][1000 genomes]
rs73688823	0.83[EUR][1000 genomes]
rs73688824	0.83[EUR][1000 genomes]
rs7833786	0.86[LWK][hapmap]
rs7837581	0.85[EUR][1000 genomes]
rs7837618	0.81[EUR][1000 genomes]
rs7839096	0.84[EUR][1000 genomes]
rs7843272	0.84[EUR][1000 genomes]
rs7843399	0.91[CEU][hapmap]
rs9656823	0.87[EUR][1000 genomes]
rs9656824	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:24 , 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	nsv1027648	chr8:87161437-87319476	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	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
6	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
7	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
8	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
9	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
10	nsv1016177	chr8:87177368-87319476	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
11	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
12	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
13	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
14	nsv1033007	chr8:87185458-87319476	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
15	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
16	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
17	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
18	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
19	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
20	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
21	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
22	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
23	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
24	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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2953524	CPNE3	cis	parietal	SCAN
rs2953524	DECR1	cis	parietal	SCAN
rs2953524	FAM82B	Cis_1M	lymphoblastoid	RTeQTL
rs2953524	CPNE3	cis	cerebellum	SCAN
rs2953524	FAM82B///LOC642197	Cis_1M	lymphoblastoid	RTeQTL
rs2953524	MMP16	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:87308400-87317800	Weak transcription	Hela-S3	cervix
2	chr8:87314000-87317400	Weak transcription	A549	lung
3	chr8:87314000-87318200	Weak transcription	Small Intestine	intestine
4	chr8:87314000-87318600	Weak transcription	Ovary	ovary
5	chr8:87315400-87317400	Weak transcription	NHEK	skin
6	chr8:87315800-87317400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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