Variant report

Variant	rs59411977
Chromosome Location	chr3:94023729-94023730
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	chr3:94021756..94024781-chr3:94027774..94031096,3	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs1031499	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11924976	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11925938	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11926658	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12637776	0.87[AFR][1000 genomes]
rs13064887	0.80[AFR][1000 genomes]
rs13317027	0.86[ASN][1000 genomes]
rs1470955	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1584923	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1584924	0.88[AFR][1000 genomes]
rs1584926	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1598219	0.87[AFR][1000 genomes]
rs1598221	0.88[AFR][1000 genomes]
rs1598222	0.89[AFR][1000 genomes]
rs1598228	0.81[AFR][1000 genomes]
rs1598232	0.81[AFR][1000 genomes]
rs1598233	0.81[AFR][1000 genomes]
rs1902103	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1902104	0.81[AFR][1000 genomes]
rs28528118	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28566994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28690421	0.82[ASN][1000 genomes]
rs34292321	0.89[AFR][1000 genomes]
rs4241463	0.88[AFR][1000 genomes]
rs4395400	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4857070	0.87[AFR][1000 genomes]
rs56212636	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56389402	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs57572900	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58561740	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59575221	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62266989	0.81[AFR][1000 genomes]
rs62266997	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs62267007	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6776344	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6782167	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6788072	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7618679	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7623613	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7623767	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7633025	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7639259	0.81[AFR][1000 genomes]
rs897182	0.81[AFR][1000 genomes]
rs897185	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs977082	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9818721	0.86[ASN][1000 genomes]
rs9819378	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9819723	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9834581	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9841043	0.82[ASN][1000 genomes]
rs9842401	0.82[ASN][1000 genomes]
rs9849065	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9855177	0.87[AFR][1000 genomes]
rs9858367	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9860831	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9863555	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9868593	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9870104	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9877808	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9883747	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869241	chr3:93527675-94504491	Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv998173	chr3:93575084-94427403	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv536644	chr3:93575084-94427403	Active TSS Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
4	nsv1008711	chr3:93575284-94427264	Flanking Active TSS Enhancers Active TSS Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv536646	chr3:93575284-94427264	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
6	nsv491829	chr3:93575285-94427263	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription 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 miRNA target site	23 gene(s)	inside rSNPs	diseases
7	nsv1013107	chr3:93654100-94102212	Enhancers Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv536648	chr3:93654100-94102212	Weak transcription Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
9	nsv1004176	chr3:93654100-94502551	Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
10	nsv877162	chr3:93779664-94278078	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Weak transcription Genic enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv877163	chr3:93795972-94047775	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
12	nsv1000265	chr3:94012384-94259057	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv536650	chr3:94012384-94259057	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv877164	chr3:94018657-94146460	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
15	nsv877165	chr3:94018657-94160736	Enhancers Weak transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:94022000-94023800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr3:94022200-94026000	Enhancers	Fetal Heart	heart
3	chr3:94022400-94024000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr3:94022400-94024000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
5	chr3:94022400-94025000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr3:94022400-94026000	Enhancers	Adipose Nuclei	Adipose
7	chr3:94022600-94024200	Enhancers	Stomach Smooth Muscle	stomach
8	chr3:94022600-94025200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:94022600-94025600	Enhancers	Rectal Smooth Muscle	rectum
10	chr3:94022600-94026000	Enhancers	Duodenum Smooth Muscle	Duodenum
11	chr3:94022800-94023800	Enhancers	Aorta	Aorta
12	chr3:94022800-94023800	Weak transcription	Fetal Intestine Large	intestine
13	chr3:94022800-94024000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:94022800-94024000	Enhancers	Fetal Muscle Leg	muscle
15	chr3:94022800-94024000	Enhancers	Ovary	ovary
16	chr3:94022800-94024600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr3:94022800-94024600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
18	chr3:94022800-94025000	Enhancers	Fetal Lung	lung
19	chr3:94022800-94025000	Weak transcription	Placenta	Placenta
20	chr3:94022800-94025800	Enhancers	HUES48 Cell Line	embryonic stem cell
21	chr3:94022800-94026000	Enhancers	Fetal Stomach	stomach
22	chr3:94023000-94025800	Enhancers	Colon Smooth Muscle	Colon
23	chr3:94023200-94024200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr3:94023200-94025000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr3:94023200-94025600	Weak transcription	Brain Angular Gyrus	brain
26	chr3:94023200-94027800	Weak transcription	Brain Hippocampus Middle	brain
27	chr3:94023400-94023800	Enhancers	Fetal Brain Female	brain
28	chr3:94023400-94024000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr3:94023400-94024000	Enhancers	Left Ventricle	heart
30	chr3:94023400-94025200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
31	chr3:94023400-94025200	Weak transcription	Fetal Brain Male	brain
32	chr3:94023400-94026000	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr3:94023600-94023800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:94023600-94024000	Enhancers	Brain Substantia Nigra	brain
35	chr3:94023600-94024000	Enhancers	Right Atrium	heart
36	chr3:94023600-94024200	Enhancers	Brain Anterior Caudate	brain
37	chr3:94023600-94024600	Weak transcription	HUES64 Cell Line	embryonic stem cell

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