Variant report

Variant	rs61574029
Chromosome Location	chr3:50558817-50558818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:50555922..50558909-chr3:50650666..50652312,2	MCF-7	breast:

Extended variants
information (count: 87 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1107312	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12486143	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12486717	0.85[AMR][1000 genomes]
rs12487817	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12489607	0.87[AMR][1000 genomes]
rs12491440	0.87[AMR][1000 genomes]
rs12491812	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12492093	0.87[AMR][1000 genomes]
rs12492540	0.87[AMR][1000 genomes]
rs12492982	0.87[AMR][1000 genomes]
rs12494094	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12494326	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17050991	0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17050995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051000	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17051043	0.87[AMR][1000 genomes]
rs17051045	0.87[AMR][1000 genomes]
rs1872184	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs1894459	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2076927	0.85[AMR][1000 genomes]
rs2170840	0.86[AMR][1000 genomes]
rs2227292	0.89[ASN][1000 genomes]
rs2227293	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2239750	0.82[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2239751	0.90[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs2239752	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2239753	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2285090	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3749265	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3752449	0.89[ASN][1000 genomes]
rs3792323	0.84[ASN][1000 genomes]
rs3806706	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4476497	0.90[AMR][1000 genomes]
rs4640555	0.95[ASN][1000 genomes]
rs4688705	0.90[AMR][1000 genomes]
rs4688707	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4688709	0.89[ASN][1000 genomes]
rs4688710	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4688713	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4688715	0.98[ASN][1000 genomes]
rs4688716	0.82[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs56170012	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56856095	0.85[AMR][1000 genomes]
rs57910827	0.87[AMR][1000 genomes]
rs58427389	0.81[ASN][1000 genomes]
rs59036236	0.85[AMR][1000 genomes]
rs60552073	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60877431	0.87[AMR][1000 genomes]
rs61193866	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61316441	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61613532	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs616689	0.90[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs6446208	0.90[AMR][1000 genomes]
rs650655	0.90[AMR][1000 genomes]
rs6766638	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6771348	0.90[AMR][1000 genomes]
rs6783922	0.90[AMR][1000 genomes]
rs6794155	0.89[AMR][1000 genomes]
rs728902	0.87[AMR][1000 genomes]
rs72938758	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs72942785	0.87[AMR][1000 genomes]
rs72942794	0.87[AMR][1000 genomes]
rs73835531	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs743753	0.90[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs745356	0.90[AMR][1000 genomes]
rs762889	0.89[ASN][1000 genomes]
rs808148	0.90[AMR][1000 genomes]
rs876103	0.90[AMR][1000 genomes]
rs876104	0.90[AMR][1000 genomes]
rs876105	0.90[AMR][1000 genomes]
rs9814874	0.82[EUR][1000 genomes]
rs9868889	0.90[AMR][1000 genomes]
rs9879397	0.90[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv523662	chr3:50144951-50584999	Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	101 gene(s)	inside rSNPs	diseases
2	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
3	nsv470561	chr3:50158774-50584999	Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
5	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
6	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
7	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
8	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
9	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
10	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
11	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
12	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
13	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
14	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50553800-50559000	Weak transcription	Brain Anterior Caudate	brain
2	chr3:50553800-50563000	Weak transcription	K562	blood
3	chr3:50554600-50559000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr3:50554600-50563200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr3:50554800-50560800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr3:50555800-50559200	Weak transcription	Spleen	Spleen
7	chr3:50556000-50563000	Weak transcription	Primary hematopoietic stem cells	blood
8	chr3:50556800-50560000	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr3:50557400-50559600	Weak transcription	Fetal Intestine Small	intestine
10	chr3:50557400-50560800	Weak transcription	Skeletal Muscle Male	skeletal muscle
11	chr3:50558000-50559600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr3:50558000-50559800	Enhancers	H1 Cell Line	embryonic stem cell
13	chr3:50558000-50559800	Enhancers	HUES48 Cell Line	embryonic stem cell
14	chr3:50558000-50560000	Enhancers	iPS-20b Cell Line	embryonic stem cell
15	chr3:50558000-50560200	Enhancers	iPS-18 Cell Line	embryonic stem cell
16	chr3:50558000-50560200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr3:50558000-50561600	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr3:50558200-50559000	Flanking Active TSS	iPS-15b Cell Line	embryonic stem cell
19	chr3:50558200-50559000	Bivalent Enhancer	Placenta	Placenta
20	chr3:50558200-50559200	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
21	chr3:50558200-50559800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr3:50558400-50559400	Enhancers	ES-WA7 Cell Line	embryonic stem cell
23	chr3:50558600-50559000	Bivalent Enhancer	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:50558600-50560200	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr3:50558600-50563000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr3:50558800-50559200	Bivalent Enhancer	NHEK	skin
27	chr3:50558800-50559600	Bivalent Enhancer	Brain Germinal Matrix	brain
28	chr3:50558800-50559800	Weak transcription	Fetal Intestine Large	intestine
29	chr3:50558800-50560800	Weak transcription	H9 Cell Line	embryonic stem cell
30	chr3:50558800-50570600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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