Variant report

Variant	rs10230508
Chromosome Location	chr7:3766622-3766623
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	chr7:3757251..3758935-chr7:3765168..3767703,2	MCF-7	breast:

Extended variants
information (count: 72 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10232073	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10233235	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10243789	0.90[EUR][1000 genomes]
rs10245274	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs10248557	0.89[CEU][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10250562	0.90[EUR][1000 genomes]
rs10251183	0.86[CEU][hapmap];0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs10253170	0.95[EUR][1000 genomes]
rs10261179	0.94[TSI][hapmap];0.95[EUR][1000 genomes]
rs10263462	0.90[EUR][1000 genomes]
rs10264235	1.00[CEU][hapmap];1.00[GIH][hapmap];0.81[LWK][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs10266535	0.82[YRI][hapmap]
rs10266883	0.89[CEU][hapmap]
rs10270665	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10271900	0.95[EUR][1000 genomes]
rs10276392	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs10480094	0.89[MEX][hapmap];0.94[TSI][hapmap];0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs17133734	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17133739	0.89[CEU][hapmap];0.89[MEX][hapmap];0.94[TSI][hapmap];0.98[EUR][1000 genomes]
rs17133774	0.89[CEU][hapmap];0.94[TSI][hapmap];0.93[EUR][1000 genomes]
rs17133778	0.88[TSI][hapmap];0.90[EUR][1000 genomes]
rs2051916	0.82[YRI][hapmap]
rs28402987	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28503504	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28708453	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41883	0.85[ASW][hapmap]
rs41888	0.85[ASW][hapmap]
rs55944228	0.90[EUR][1000 genomes]
rs56111663	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs58744635	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs59839518	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs61173285	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62437932	0.86[EUR][1000 genomes]
rs6462250	0.88[CEU][hapmap];0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6945690	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6946053	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6952117	0.86[CEU][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6953733	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6958764	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6959206	0.90[EUR][1000 genomes]
rs6963031	0.82[YRI][hapmap]
rs6967060	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6970399	1.00[CEU][hapmap];0.83[LWK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6972186	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6972653	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6978942	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6979251	0.91[ASW][hapmap];0.88[GIH][hapmap];0.92[LWK][hapmap];0.89[YRI][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6980175	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs6980395	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73304214	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs73304218	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7776614	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7785239	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7795719	0.95[EUR][1000 genomes]
rs7802557	0.82[YRI][hapmap];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs7803963	0.87[CEU][hapmap];0.89[MEX][hapmap];0.88[TSI][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1018173	chr7:3258989-3879848	Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	nsv538660	chr7:3258989-3879848	Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1016555	chr7:3298478-3872512	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv538661	chr7:3298478-3872512	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv830888	chr7:3577214-3776276	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv1021650	chr7:3665232-4577439	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv1017868	chr7:3698885-3820159	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
8	nsv887335	chr7:3700352-3766819	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
9	nsv1021443	chr7:3705273-3889334	ZNF genes & repeats Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	nsv605935	chr7:3713194-3799580	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
11	nsv1019582	chr7:3718061-3814514	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
12	nsv538682	chr7:3718061-3814514	Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
13	nsv605936	chr7:3722433-3766819	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
14	nsv1022650	chr7:3723035-3847680	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv1024704	chr7:3736254-3831859	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1031610	chr7:3744536-3838844	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:3755200-3770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:3762400-3777000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr7:3762800-3770000	Weak transcription	Brain Substantia Nigra	brain
4	chr7:3763000-3772800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:3764200-3766800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr7:3764400-3766800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr7:3765200-3769600	Weak transcription	Brain Angular Gyrus	brain
8	chr7:3765400-3769000	Weak transcription	Fetal Muscle Leg	muscle
9	chr7:3765400-3769600	Weak transcription	Brain Cingulate Gyrus	brain
10	chr7:3765400-3769800	Weak transcription	Brain Hippocampus Middle	brain
11	chr7:3765400-3769800	Weak transcription	Fetal Stomach	stomach
12	chr7:3765600-3769400	Weak transcription	Fetal Lung	lung
13	chr7:3765600-3769800	Weak transcription	Brain Anterior Caudate	brain
14	chr7:3766200-3766800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
15	chr7:3766200-3766800	Enhancers	Ovary	ovary
16	chr7:3766600-3766800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr7:3766600-3767200	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood

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