Variant report

Variant	rs3820058
Chromosome Location	chr1:169195168-169195169
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	chr1:169193895..169196797-chr1:169197836..169199358,2	MCF-7	breast:

Extended variants
information (count: 58 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10158265	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10158861	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919088	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10919102	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10919146	0.97[ASN][1000 genomes]
rs11808274	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs11809378	0.87[ASN][1000 genomes]
rs12023291	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12025233	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12026996	0.95[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12029853	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12032783	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12033078	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12035804	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12036968	0.82[AFR][1000 genomes]
rs12037211	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12038609	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12039443	1.00[ASN][1000 genomes]
rs12040813	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs12043489	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12043545	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12045202	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12046139	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12047231	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1415928	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1589113	0.93[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16828170	0.85[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs2268048	1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34710865	0.88[ASN][1000 genomes]
rs3766058	0.84[EUR][1000 genomes]
rs3766089	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56341747	0.98[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs58585501	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs61806986	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808865	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61808901	0.82[AFR][1000 genomes];0.82[ASN][1000 genomes]
rs61808903	0.81[ASN][1000 genomes]
rs61808914	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61808915	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6664272	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6685556	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6698149	0.84[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs7521338	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9633334	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9804101	0.86[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs9988595	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9988604	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
2	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases
4	nsv429913	chr1:169177019-169296744	Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	esv1834321	chr1:169180302-169240975	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	esv1845262	chr1:169180302-169240975	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv1010010	chr1:169189586-169347545	Active TSS Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
8	nsv525520	chr1:169191860-169240084	Enhancers Flanking Active TSS Weak transcription Genic enhancers ZNF genes & repeats Active TSS Strong transcription	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	esv1845267	chr1:169191860-169240975	Enhancers Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	esv1849515	chr1:169191860-169240975	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv872531	chr1:169191860-169388193	Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169130400-169195200	Weak transcription	Pancreas	Pancrea
2	chr1:169172400-169207600	Weak transcription	Esophagus	oesophagus
3	chr1:169172600-169227000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr1:169173200-169202000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr1:169176600-169206200	Weak transcription	Aorta	Aorta
6	chr1:169177400-169207400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:169180000-169210000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr1:169180600-169206200	Weak transcription	Left Ventricle	heart
9	chr1:169182000-169201000	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr1:169182800-169205400	Weak transcription	Adipose Nuclei	Adipose
11	chr1:169184000-169198800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:169184400-169206200	Weak transcription	Lung	lung
13	chr1:169184600-169200600	Weak transcription	Fetal Stomach	stomach
14	chr1:169184800-169207400	Weak transcription	Ovary	ovary
15	chr1:169185000-169200800	Weak transcription	Fetal Intestine Small	intestine
16	chr1:169187600-169200200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
17	chr1:169187600-169207800	Weak transcription	Primary T cells from cord blood	blood
18	chr1:169187800-169211800	Weak transcription	Primary hematopoietic stem cells	blood
19	chr1:169191600-169198400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr1:169192200-169209600	Weak transcription	NHEK	skin
21	chr1:169192400-169210000	Weak transcription	Brain Hippocampus Middle	brain
22	chr1:169192600-169202800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr1:169193000-169196800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
24	chr1:169194000-169210000	Weak transcription	NHDF-Ad	bronchial
25	chr1:169194600-169198400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:169194800-169200600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr1:169194800-169207400	Weak transcription	Primary B cells from cord blood	blood
28	chr1:169194800-169214000	Weak transcription	Sigmoid Colon	Sigmoid Colon

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