Variant report

Variant	rs9504009
Chromosome Location	chr6:4255905-4255906
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	chr6:4252767..4255076-chr6:4255779..4258262,2	MCF-7	breast:

Extended variants
information (count: 119 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:96)

rs_ID	r²[population]
rs10080414	0.88[EUR][1000 genomes]
rs10223886	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10428864	0.87[EUR][1000 genomes]
rs1072903	0.88[EUR][1000 genomes]
rs11756906	1.00[JPT][hapmap]
rs11961149	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970375	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11970430	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1591412	0.89[EUR][1000 genomes]
rs17500205	0.94[EUR][1000 genomes]
rs17538963	0.80[EUR][1000 genomes]
rs17565229	0.95[EUR][1000 genomes]
rs1832060	0.89[EUR][1000 genomes]
rs2210761	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2210762	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2326473	0.89[EUR][1000 genomes]
rs4255019	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4256473	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4317452	0.80[EUR][1000 genomes]
rs4354197	0.80[EUR][1000 genomes]
rs4443539	0.98[EUR][1000 genomes]
rs4475361	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4526241	0.89[EUR][1000 genomes]
rs4596533	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4629733	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4959937	0.88[EUR][1000 genomes]
rs4959938	0.88[EUR][1000 genomes]
rs57509474	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs58402712	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs59706955	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60023788	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61604146	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6597046	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6597047	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6597048	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6913742	0.89[EUR][1000 genomes]
rs6916181	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6922330	0.88[EUR][1000 genomes]
rs6931784	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6934489	0.90[EUR][1000 genomes]
rs6934652	0.90[EUR][1000 genomes]
rs73356806	0.80[EUR][1000 genomes]
rs73358820	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73358823	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73358854	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs73360930	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73360933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs73360945	0.99[EUR][1000 genomes]
rs7754298	0.95[EUR][1000 genomes]
rs7759565	0.88[EUR][1000 genomes]
rs7763657	0.96[AFR][1000 genomes];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7763789	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7765457	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs913405	0.94[EUR][1000 genomes]
rs9328227	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328229	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328230	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9328231	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328232	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328233	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9328236	0.99[EUR][1000 genomes]
rs9392032	0.90[EUR][1000 genomes]
rs9392578	0.86[EUR][1000 genomes]
rs9392580	0.88[EUR][1000 genomes]
rs9405228	0.90[EUR][1000 genomes]
rs9502148	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502149	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502150	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9502151	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502152	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9502153	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9502154	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9502157	0.99[EUR][1000 genomes]
rs9502158	0.99[EUR][1000 genomes]
rs9502159	0.99[EUR][1000 genomes]
rs9502160	0.98[EUR][1000 genomes]
rs9502161	0.93[EUR][1000 genomes]
rs9502163	0.94[EUR][1000 genomes]
rs9503948	0.80[EUR][1000 genomes]
rs9503953	0.80[EUR][1000 genomes]
rs9503982	0.89[EUR][1000 genomes]
rs9503983	0.89[EUR][1000 genomes]
rs9503984	0.89[EUR][1000 genomes]
rs9503985	0.86[EUR][1000 genomes]
rs9503993	0.96[EUR][1000 genomes]
rs9503994	0.96[EUR][1000 genomes]
rs9503995	0.96[EUR][1000 genomes]
rs9503996	0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9504005	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9504006	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs9504007	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504008	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9504010	1.00[EUR][1000 genomes]
rs9504022	0.99[EUR][1000 genomes]
rs9504025	0.94[EUR][1000 genomes]
rs9504033	0.95[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:23 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1022968	chr6:3862744-4272502	Enhancers Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
2	nsv538106	chr6:3862744-4272502	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
3	esv2422457	chr6:4100333-4377396	Enhancers Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv600861	chr6:4238488-4469641	Enhancers Weak transcription Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	nsv462618	chr6:4238488-4472587	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv600862	chr6:4238488-4472587	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
7	nsv949364	chr6:4253413-4466981	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
8	esv17585	chr6:4254023-4257185	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv600863	chr6:4255387-4472587	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
10	nsv1027498	chr6:4255640-4471635	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
11	esv2763995	chr6:4255640-4474114	Bivalent/Poised TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
12	nsv1020205	chr6:4255640-4474114	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv600864	chr6:4255708-4464630	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv516402	chr6:4255708-4472587	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv462619	chr6:4255708-4472587	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv600865	chr6:4255708-4472587	Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv462620	chr6:4255708-4481421	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv600866	chr6:4255708-4481421	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
19	nsv600867	chr6:4255725-4464630	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
20	nsv462621	chr6:4255725-4472587	Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
21	nsv600868	chr6:4255725-4472587	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
22	nsv1029501	chr6:4255745-4471635	Enhancers Active TSS Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
23	nsv432845	chr6:4255905-4471472	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9504009	PECI	cis	cerebellum	SCAN
rs9504009	CDYL	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4254200-4259000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr6:4254400-4258000	Weak transcription	Lung	lung
3	chr6:4254600-4256800	Weak transcription	Placenta	Placenta
4	chr6:4254600-4258200	Weak transcription	Left Ventricle	heart
5	chr6:4254600-4259600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
6	chr6:4254800-4256800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr6:4254800-4258200	Weak transcription	Right Atrium	heart
8	chr6:4254800-4258800	Weak transcription	NHEK	skin
9	chr6:4254800-4259000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr6:4255000-4256800	Weak transcription	HUVEC	blood vessel
11	chr6:4255400-4258400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr6:4255600-4256000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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