Variant report

Variant	rs3819389
Chromosome Location	chr4:55526920-55526921
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:55526044..55527656-chr4:55529218..55531772,2	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:36)

rs_ID	r²[population]
rs1005438	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11733357	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12503461	0.90[GIH][hapmap]
rs13119906	1.00[JPT][hapmap]
rs13128858	0.92[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes]
rs13135792	0.86[CHB][hapmap]
rs13147869	0.84[GIH][hapmap];1.00[JPT][hapmap];0.96[MEX][hapmap];0.89[TSI][hapmap]
rs17827974	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2017472	0.90[GIH][hapmap]
rs2237028	0.82[CEU][hapmap]
rs2237031	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2237035	0.85[CHB][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2282778	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.90[TSI][hapmap];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282779	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2282780	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2282781	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703456	0.80[EUR][1000 genomes]
rs34284864	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35441406	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3756197	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3819387	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3819392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3822213	0.95[CEU][hapmap];0.84[CHB][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864915	1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6554196	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6820303	0.88[GIH][hapmap]
rs6825657	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs71599647	0.81[EUR][1000 genomes]
rs759082	0.80[EUR][1000 genomes]
rs759083	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[GIH][hapmap];0.83[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes]
rs7655556	0.81[EUR][1000 genomes]
rs7655588	0.81[EUR][1000 genomes]
rs7656858	0.81[EUR][1000 genomes]
rs7675203	0.81[EUR][1000 genomes]
rs7684000	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7697799	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008793	chr4:55060925-55535807	Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv537098	chr4:55060925-55535807	Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv999400	chr4:55143598-55776995	Enhancers Weak transcription Bivalent Enhancer Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv997430	chr4:55253397-55529288	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	esv3367952	chr4:55437113-55724644	Bivalent/Poised TSS Strong transcription Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv1010702	chr4:55440944-55528450	Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv526344	chr4:55522488-56231119	Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3819389	SRD5A3	cis	cerebellum	SCAN

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:55523000-55528600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr4:55524800-55527200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr4:55525200-55527400	Flanking Active TSS	Primary hematopoietic stem cells	blood
4	chr4:55525800-55527000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr4:55525800-55528600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr4:55525800-55528600	Enhancers	NHLF	lung
7	chr4:55525800-55529200	Weak transcription	Aorta	Aorta
8	chr4:55525800-55537200	Weak transcription	Right Atrium	heart
9	chr4:55526000-55527000	Enhancers	Breast Myoepithelial Primary Cells	Breast
10	chr4:55526000-55527800	Enhancers	Psoas Muscle	Psoas
11	chr4:55526000-55528600	Enhancers	NH-A	brain
12	chr4:55526200-55527200	Bivalent Enhancer	Fetal Brain Male	brain
13	chr4:55526200-55527600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr4:55526200-55527800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
15	chr4:55526400-55527000	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
16	chr4:55526400-55527400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr4:55526400-55527600	Enhancers	NHEK	skin
18	chr4:55526400-55527800	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr4:55526400-55528200	Weak transcription	Fetal Muscle Trunk	muscle
20	chr4:55526400-55528600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr4:55526400-55528600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr4:55526600-55527000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr4:55526600-55527000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr4:55526600-55527200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr4:55526600-55527200	Enhancers	Primary hematopoietic stem cells short term culture	blood
26	chr4:55526600-55527200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr4:55526600-55527600	Weak transcription	Ovary	ovary
28	chr4:55526600-55527800	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
29	chr4:55526600-55528600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr4:55526600-55531600	Weak transcription	Gastric	stomach
31	chr4:55526800-55527200	Enhancers	NHDF-Ad	bronchial
32	chr4:55526800-55528400	Enhancers	HMEC	breast
33	chr4:55526800-55528600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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