Variant report

Variant	rs6445843
Chromosome Location	chr3:51120404-51120405
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	chr3:50899377..50900293-chr3:51119563..51120417,2	MCF-7	breast:

Extended variants
information (count: 145 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:142)

rs_ID	r²[population]
rs10212240	0.90[ASN][1000 genomes]
rs11130273	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11130274	0.90[ASN][1000 genomes]
rs11715556	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11919932	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12494165	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12630889	0.90[ASN][1000 genomes]
rs13060972	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13080170	0.81[EUR][1000 genomes]
rs28470684	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28670710	0.85[ASN][1000 genomes]
rs35356497	0.81[EUR][1000 genomes]
rs4130474	0.85[ASN][1000 genomes]
rs4244697	0.85[ASN][1000 genomes]
rs4244699	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244700	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244701	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244702	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244703	0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4244704	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4244705	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4263323	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4267674	0.85[ASN][1000 genomes]
rs4269109	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4286453	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4289378	0.90[ASN][1000 genomes]
rs4293735	0.90[ASN][1000 genomes]
rs4309762	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4309763	0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4317135	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4328835	0.90[ASN][1000 genomes]
rs4353834	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4359843	0.90[ASN][1000 genomes]
rs4377512	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4378999	0.85[ASN][1000 genomes]
rs4390967	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4422345	0.90[ASN][1000 genomes]
rs4434173	0.81[EUR][1000 genomes]
rs4438692	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4444745	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4446244	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4464493	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4465974	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4478114	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4487270	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4488874	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4491946	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4505743	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4507294	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511930	0.92[ASN][1000 genomes]
rs4511931	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4511933	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4530566	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4532165	0.90[ASN][1000 genomes]
rs4541436	0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4557193	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4572801	0.80[EUR][1000 genomes]
rs4574329	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4582086	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4586852	0.88[AMR][1000 genomes]
rs4586853	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4589968	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4596182	0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4613496	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4615113	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4639007	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927957	0.87[ASN][1000 genomes]
rs4927958	0.85[ASN][1000 genomes]
rs4927959	0.85[ASN][1000 genomes]
rs4927960	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927964	0.87[ASN][1000 genomes]
rs4927965	0.87[ASN][1000 genomes]
rs4927967	0.90[ASN][1000 genomes]
rs4927971	0.82[ASN][1000 genomes]
rs4927976	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927977	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4927978	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927979	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927980	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927982	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927983	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4927984	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4927986	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445393	0.90[ASN][1000 genomes]
rs6445455	0.85[ASN][1000 genomes]
rs6445600	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445603	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445717	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6445750	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445779	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6445802	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446011	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446118	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446167	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6446168	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6767329	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6768601	0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6769957	0.90[ASN][1000 genomes]
rs6772664	0.85[ASN][1000 genomes]
rs6775483	0.90[ASN][1000 genomes]
rs6777719	0.85[ASN][1000 genomes]
rs6779658	0.85[ASN][1000 genomes]
rs6787773	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793613	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793648	0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795272	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797368	0.90[ASN][1000 genomes]
rs6799211	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6803672	0.90[ASN][1000 genomes]
rs6806090	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6808206	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809524	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7610901	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7611873	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614785	0.94[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs7615291	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7629420	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7629433	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7630616	0.90[ASN][1000 genomes]
rs7630730	0.90[ASN][1000 genomes]
rs7639161	0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7640263	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7643781	0.95[ASN][1000 genomes]
rs7652655	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7652818	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7653451	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7653539	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9284887	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9284888	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9713035	0.82[AMR][1000 genomes]
rs9713241	0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9818841	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9827072	0.85[ASN][1000 genomes]
rs9828200	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9839860	0.90[ASN][1000 genomes]
rs9841339	0.90[ASN][1000 genomes]
rs9850021	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9857727	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9860862	0.80[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9865363	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9867256	0.85[ASN][1000 genomes]
rs9871539	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv491647	chr3:50856276-51245158	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1005858	chr3:51090373-51444027	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases
3	nsv536569	chr3:51090373-51444027	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:51110600-51121400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr3:51113200-51121000	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr3:51118200-51129400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr3:51119200-51124000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr3:51119400-51120800	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
6	chr3:51119400-51121000	Strong transcription	Brain Hippocampus Middle	brain
7	chr3:51119400-51121400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
8	chr3:51119600-51120600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr3:51119600-51120600	Strong transcription	Brain Inferior Temporal Lobe	brain
10	chr3:51119600-51120800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr3:51119600-51120800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr3:51119600-51122800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
13	chr3:51119800-51120600	ZNF genes & repeats	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr3:51119800-51121000	ZNF genes & repeats	Fetal Brain Female	brain
15	chr3:51120000-51120800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
16	chr3:51120000-51120800	ZNF genes & repeats	Brain Angular Gyrus	brain
17	chr3:51120000-51120800	ZNF genes & repeats	Brain Dorsolateral Prefrontal Cortex	brain
18	chr3:51120200-51120600	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr3:51120200-51120600	ZNF genes & repeats	Brain Substantia Nigra	brain
20	chr3:51120400-51120600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
21	chr3:51120400-51121000	ZNF genes & repeats	Fetal Brain Male	brain

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