Variant report

Variant	rs9876543
Chromosome Location	chr3:110623293-110623294
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	chr3:110617155..110618688-chr3:110622142..110624409,2	MCF-7	breast:

Extended variants
information (count: 78 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10049325	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10511290	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1075303	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11927478	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13080214	0.91[ASN][1000 genomes]
rs13093547	0.80[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1350980	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1381828	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1462325	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1462789	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1462790	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1462793	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1462795	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1462801	0.94[ASN][1000 genomes]
rs1462807	0.92[ASN][1000 genomes]
rs1477846	0.87[CEU][hapmap]
rs1477847	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap]
rs1477848	0.87[CEU][hapmap]
rs1564056	0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1580288	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1585594	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1585595	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1599663	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1599664	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16857483	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1824666	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1903755	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1903759	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1993802	0.94[ASN][1000 genomes]
rs1993803	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2002969	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2100875	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2399367	0.94[ASN][1000 genomes]
rs2399368	0.94[ASN][1000 genomes]
rs2399370	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2399371	0.95[ASN][1000 genomes]
rs2399373	0.87[CEU][hapmap];0.86[CHB][hapmap];0.87[YRI][hapmap]
rs2399378	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2895376	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35665971	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4102676	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4234401	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682028	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4682212	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4682215	0.94[ASN][1000 genomes]
rs4682229	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap]
rs4682230	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap]
rs4682231	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap]
rs5000277	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6437940	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs66513024	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67056469	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs67832786	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6787921	0.94[ASN][1000 genomes]
rs6805399	0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6808847	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71618767	0.89[ASN][1000 genomes]
rs723023	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs723025	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7612667	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap]
rs7622983	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7623003	0.94[ASN][1000 genomes]
rs7623064	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7623103	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7637068	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7644948	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9817950	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9821335	0.87[CEU][hapmap];0.91[CHB][hapmap];0.81[YRI][hapmap]
rs9826064	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9828899	0.87[CEU][hapmap];0.91[CHB][hapmap];0.87[YRI][hapmap]
rs9839299	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9839674	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9874206	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9876350	0.88[CEU][hapmap];0.91[CHB][hapmap];0.88[YRI][hapmap]

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	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	esv2762345	chr3:110614389-110668843	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
4	nsv829674	chr3:110616256-110771049	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110611400-110628600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:110612600-110635600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr3:110620200-110653800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:110621600-110625000	Weak transcription	Fetal Muscle Leg	muscle
5	chr3:110622600-110623400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr3:110622600-110623400	Enhancers	Brain Hippocampus Middle	brain
7	chr3:110622600-110623400	Enhancers	Fetal Heart	heart
8	chr3:110622600-110623600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr3:110622800-110623600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:110623000-110624000	Enhancers	Brain Substantia Nigra	brain
11	chr3:110623200-110627200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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