Variant report

Variant	rs3789423
Chromosome Location	chr1:94566496-94566497
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:94564366..94567195-chr1:94607779..94609670,2	MCF-7	breast:
2	chr1:94533904..94535691-chr1:94564792..94567232,2	MCF-7	breast:
3	chr1:94565431..94568158-chr1:94701481..94704374,2	MCF-7	breast:
4	chr1:94565667..94567409-chr1:94572169..94573688,2	MCF-7	breast:
5	chr1:94564934..94567258-chr1:94582385..94584556,2	MCF-7	breast:
6	chr1:94560214..94561880-chr1:94564179..94567111,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000137962	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12074537	1.00[YRI][hapmap]
rs3789422	1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3789424	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6657239	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7513438	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv871057	chr1:94513142-94577286	ZNF genes & repeats Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv871558	chr1:94544276-94576968	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
3	nsv870555	chr1:94545160-94577744	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	n/a
4	esv1807674	chr1:94549175-94588191	Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
5	nsv871416	chr1:94566311-94635028	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:94555600-94570000	Enhancers	Fetal Thymus	thymus
2	chr1:94558200-94573000	Weak transcription	Spleen	Spleen
3	chr1:94560800-94570000	Weak transcription	Pancreas	Pancrea
4	chr1:94560800-94570800	Weak transcription	Thymus	Thymus
5	chr1:94561200-94568800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr1:94561200-94569800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:94561200-94570400	Weak transcription	Dnd41	blood
8	chr1:94561600-94571400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr1:94562600-94566800	Weak transcription	Brain Angular Gyrus	brain
10	chr1:94562800-94566800	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr1:94563200-94570000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr1:94563400-94566800	Weak transcription	Fetal Lung	lung
13	chr1:94564000-94572600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:94564200-94573000	Enhancers	Placenta Amnion	Placenta Amnion
15	chr1:94564400-94566600	Enhancers	Lung	lung
16	chr1:94564600-94568000	Enhancers	Fetal Kidney	kidney
17	chr1:94564600-94570000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:94564600-94570400	Weak transcription	Left Ventricle	heart
19	chr1:94564600-94573600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:94564600-94591800	Weak transcription	Right Atrium	heart
21	chr1:94564800-94577400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr1:94565000-94570600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:94565200-94570400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr1:94565400-94566600	Enhancers	Colon Smooth Muscle	Colon
25	chr1:94565400-94567400	Enhancers	Rectal Smooth Muscle	rectum
26	chr1:94565400-94572400	Enhancers	Placenta	Placenta
27	chr1:94565800-94566800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr1:94566200-94566800	Enhancers	NHEK	skin
29	chr1:94566200-94567200	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr1:94566200-94567200	Enhancers	HUVEC	blood vessel
31	chr1:94566200-94567400	Enhancers	Brain Anterior Caudate	brain
32	chr1:94566200-94567400	Bivalent Enhancer	HepG2	liver
33	chr1:94566200-94568200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr1:94566200-94571800	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr1:94566400-94566600	Bivalent Enhancer	Colonic Mucosa	Colon
36	chr1:94566400-94566800	Enhancers	Fetal Heart	heart
37	chr1:94566400-94567200	Weak transcription	HUES6 Cell Line	embryonic stem cell
38	chr1:94566400-94567200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr1:94566400-94567200	Enhancers	Ovary	ovary
40	chr1:94566400-94567600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr1:94566400-94567600	Bivalent Enhancer	Fetal Stomach	stomach
42	chr1:94566400-94567800	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr1:94566400-94567800	Enhancers	HMEC	breast

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