Variant report

Variant	rs13100499
Chromosome Location	chr3:23491444-23491445
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	chr3:23489983..23492292-chr3:23500438..23503341,2	MCF-7	breast:
2	chr3:23489870..23492697-chr3:23493234..23495139,2	MCF-7	breast:

Extended variants
information (count: 122 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:118)

rs_ID	r²[population]
rs12106681	0.86[EUR][1000 genomes]
rs13059155	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13059557	0.81[EUR][1000 genomes]
rs13060112	1.00[CEU][hapmap]
rs13060251	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13063451	1.00[CEU][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13065375	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13065646	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs13066741	0.91[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13067514	1.00[CEU][hapmap]
rs13070136	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13071171	0.98[EUR][1000 genomes]
rs13072325	1.00[CEU][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13073761	0.95[EUR][1000 genomes]
rs13076412	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs13076527	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs13078970	0.86[EUR][1000 genomes]
rs13082311	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13084870	1.00[CEU][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13085173	1.00[CEU][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13085266	0.95[EUR][1000 genomes]
rs13087238	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs13087563	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs13088756	1.00[EUR][1000 genomes]
rs13090125	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13090335	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13090633	0.85[EUR][1000 genomes]
rs13091625	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13091634	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13092830	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs13095737	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13096187	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13098798	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13100605	0.86[EUR][1000 genomes]
rs17013241	1.00[YRI][hapmap]
rs34134134	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34171096	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34225647	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34322396	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34443476	0.88[EUR][1000 genomes]
rs34474714	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34504120	0.87[EUR][1000 genomes]
rs34584255	0.86[EUR][1000 genomes]
rs34619482	0.95[EUR][1000 genomes]
rs34732257	0.95[EUR][1000 genomes]
rs34743949	0.89[EUR][1000 genomes]
rs34758087	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34804976	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34827773	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34882744	0.97[EUR][1000 genomes]
rs34894979	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34896901	0.87[AFR][1000 genomes]
rs34916096	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34916962	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs34928966	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs34970845	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35021696	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35027557	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35028631	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35055753	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35096750	0.86[EUR][1000 genomes]
rs35105861	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35121170	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35152860	0.98[EUR][1000 genomes]
rs35156003	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35177750	1.00[EUR][1000 genomes]
rs35179250	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35190363	0.95[EUR][1000 genomes]
rs35209889	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35218978	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35230557	0.95[EUR][1000 genomes]
rs35240920	0.86[EUR][1000 genomes]
rs35245309	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35266274	0.85[EUR][1000 genomes]
rs35273607	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35314441	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35346188	0.86[EUR][1000 genomes]
rs35347265	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35383024	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs35402533	0.89[EUR][1000 genomes]
rs35408638	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35497505	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35587590	0.86[EUR][1000 genomes]
rs35649850	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs35657558	0.89[EUR][1000 genomes]
rs35776486	0.86[EUR][1000 genomes]
rs35778452	1.00[EUR][1000 genomes]
rs35869522	0.89[EUR][1000 genomes]
rs35902312	0.95[EUR][1000 genomes]
rs35907941	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35928592	0.95[EUR][1000 genomes]
rs35975795	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36021750	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs36082634	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36123979	0.86[EUR][1000 genomes]
rs36124326	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs36183485	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs58522464	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60074421	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71317827	0.86[EUR][1000 genomes]
rs71317829	0.86[EUR][1000 genomes]
rs71317834	0.81[EUR][1000 genomes]
rs71322171	0.89[EUR][1000 genomes]
rs71322172	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322173	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs71322174	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322183	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322184	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322185	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322187	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322189	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71322190	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71322195	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs71322200	0.91[EUR][1000 genomes]
rs71322201	0.97[EUR][1000 genomes]
rs71322202	0.97[EUR][1000 genomes]
rs71324103	0.88[EUR][1000 genomes]
rs71324104	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002823	chr3:23277838-23623083	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1007373	chr3:23367952-23710331	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv876625	chr3:23390301-23509597	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv533980	chr3:23445901-24311972	ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	64 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:23473800-23494000	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr3:23484800-23496000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr3:23484800-23496000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
4	chr3:23485200-23496400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr3:23485200-23498600	Weak transcription	Primary T helper cells PMA-I stimulated	--
6	chr3:23486200-23494000	Weak transcription	HSMMtube	muscle
7	chr3:23488600-23496000	Weak transcription	Fetal Heart	heart
8	chr3:23488600-23496200	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr3:23488600-23496400	Weak transcription	Ovary	ovary
10	chr3:23489800-23496400	Weak transcription	Right Ventricle	heart
11	chr3:23490200-23491800	Enhancers	Brain Substantia Nigra	brain
12	chr3:23490600-23491600	Enhancers	Primary B cells from cord blood	blood
13	chr3:23490600-23491800	Enhancers	Brain Hippocampus Middle	brain
14	chr3:23491000-23491800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr3:23491200-23491600	Enhancers	Psoas Muscle	Psoas
16	chr3:23491200-23491600	Enhancers	GM12878-XiMat	blood
17	chr3:23491200-23491600	Enhancers	NHDF-Ad	bronchial
18	chr3:23491400-23491600	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr3:23491400-23491600	Enhancers	Brain Inferior Temporal Lobe	brain
20	chr3:23491400-23491800	Enhancers	Brain Cingulate Gyrus	brain

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