Variant report

Variant	rs1980984
Chromosome Location	chr13:38940894-38940895
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:36918448..36921379-chr13:38939696..38941798,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000133104	Chromatin interaction
ENSG00000120664	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10514844	1.00[CEU][hapmap]
rs11693	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330958	1.00[CEU][hapmap];1.00[CHB][hapmap];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330960	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330963	1.00[CHB][hapmap]
rs1330964	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330965	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330976	1.00[CEU][hapmap]
rs1360385	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1553300	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576610	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1576611	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2019520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2150469	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231323	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231328	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231330	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2231331	1.00[CEU][hapmap]
rs2231332	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2455412	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481876	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481877	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481879	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2481880	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485783	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485785	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2485789	1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496456	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496466	1.00[CHB][hapmap]
rs2496473	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496475	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2496476	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943581	0.83[ASN][1000 genomes]
rs4943583	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943584	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943585	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4943586	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563608	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6563609	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326028	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7326913	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7332974	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7335723	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7338958	0.85[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285122	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532209	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9532217	0.90[AFR][1000 genomes]
rs9532218	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548318	1.00[CEU][hapmap];1.00[CHB][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9548320	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9603368	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986773	1.00[CHB][hapmap];1.00[EUR][1000 genomes];1.00[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	nsv915901	chr13:38199035-39032633	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv869125	chr13:38550449-39132813	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	10 gene(s)	inside rSNPs	diseases
3	nsv949406	chr13:38561474-39033484	Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
4	nsv900006	chr13:38924871-38970825	Genic enhancers ZNF genes & repeats Bivalent Enhancer Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
5	esv1851668	chr13:38928976-38948851	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:38926200-38947000	Weak transcription	Ovary	ovary
2	chr13:38926200-38947000	Weak transcription	Hela-S3	cervix
3	chr13:38927400-38943200	Weak transcription	K562	blood
4	chr13:38931400-38941000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr13:38933600-38943000	Weak transcription	Fetal Heart	heart
6	chr13:38936400-38941200	Weak transcription	NHLF	lung
7	chr13:38936400-38947200	Weak transcription	HepG2	liver
8	chr13:38937600-38941000	Weak transcription	HMEC	breast
9	chr13:38937800-38941000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr13:38938000-38941000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr13:38938000-38941000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr13:38938000-38941000	Weak transcription	HUVEC	blood vessel
13	chr13:38938000-38941000	Weak transcription	NHEK	skin
14	chr13:38938000-38941000	Weak transcription	Osteobl	bone
15	chr13:38938000-38941600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr13:38938000-38943200	Weak transcription	Fetal Brain Female	brain
17	chr13:38938000-38943400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr13:38938000-38946800	Weak transcription	Liver	Liver
19	chr13:38938000-38947000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr13:38938000-38947200	Weak transcription	Fetal Kidney	kidney
21	chr13:38938200-38941000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr13:38939800-38942000	Enhancers	NHDF-Ad	bronchial
23	chr13:38940400-38942000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
24	chr13:38940400-38944800	Weak transcription	Primary hematopoietic stem cells	blood
25	chr13:38940600-38941200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr13:38940600-38943800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr13:38940800-38942400	Enhancers	Muscle Satellite Cultured Cells	--
28	chr13:38940800-38943200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
29	chr13:38940800-38943200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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