Variant report

Variant	rs16999872
Chromosome Location	chr20:53247280-53247281
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53242261..53247525-chr20:53253994..53258088,8	MCF-7	breast:
2	chr20:52852335..52854423-chr20:53245467..53248244,2	MCF-7	breast:
3	chr20:53226045..53227848-chr20:53245304..53248217,2	MCF-7	breast:
4	chr20:53238250..53239788-chr20:53246518..53248056,2	MCF-7	breast:
5	chr20:52824443..52826039-chr20:53246176..53249112,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs2224269	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs28663252	1.00[ASN][1000 genomes]
rs2870331	1.00[ASN][1000 genomes]
rs2870332	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs2904386	1.00[ASN][1000 genomes]
rs4324376	1.00[ASN][1000 genomes]
rs4542911	1.00[ASN][1000 genomes]
rs4581960	1.00[ASN][1000 genomes]
rs4809968	1.00[ASN][1000 genomes]
rs4811510	1.00[ASN][1000 genomes]
rs4811511	1.00[ASN][1000 genomes]
rs4811512	0.92[CEU][hapmap]
rs4811513	1.00[ASN][1000 genomes]
rs4996783	1.00[ASN][1000 genomes]
rs58298733	1.00[ASN][1000 genomes]
rs60030360	1.00[ASN][1000 genomes]
rs6014078	1.00[ASN][1000 genomes]
rs6014080	1.00[ASN][1000 genomes]
rs6023397	1.00[ASN][1000 genomes]
rs6023398	1.00[ASN][1000 genomes]
rs6023400	1.00[ASN][1000 genomes]
rs6023401	1.00[ASN][1000 genomes]
rs6023403	1.00[ASN][1000 genomes]
rs6023406	1.00[ASN][1000 genomes]
rs6023408	1.00[ASN][1000 genomes]
rs6023409	1.00[ASN][1000 genomes]
rs6023410	1.00[ASN][1000 genomes]
rs6023428	1.00[ASN][1000 genomes]
rs6023430	1.00[ASN][1000 genomes]
rs6064092	1.00[CEU][hapmap];0.83[EUR][1000 genomes]
rs6064093	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6068916	1.00[ASN][1000 genomes]
rs6068919	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6068920	1.00[CEU][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6068923	0.94[CEU][hapmap];0.91[EUR][1000 genomes]
rs6091928	1.00[ASN][1000 genomes]
rs6091931	1.00[ASN][1000 genomes]
rs6098103	1.00[ASN][1000 genomes]
rs6098105	1.00[ASN][1000 genomes]
rs6098108	0.83[CEU][hapmap];1.00[ASN][1000 genomes]
rs6098120	1.00[ASN][1000 genomes]
rs7261209	1.00[ASN][1000 genomes]
rs7263678	1.00[ASN][1000 genomes]
rs7263680	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7269966	1.00[ASN][1000 genomes]
rs7270451	1.00[CEU][hapmap];0.85[YRI][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7270971	0.91[CEU][hapmap]
rs8115071	1.00[CEU][hapmap];0.93[YRI][hapmap];0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs967377	1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv586224	chr20:52474850-53279490	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	338 gene(s)	inside rSNPs	diseases
2	nsv1067497	chr20:53146241-53751820	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
3	nsv1064144	chr20:53175264-53750137	Enhancers Bivalent Enhancer Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
4	nsv544302	chr20:53175264-53750137	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	66 gene(s)	inside rSNPs	diseases
5	nsv586282	chr20:53218978-53254815	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	nsv1060552	chr20:53234716-53655115	Bivalent Enhancer Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53235200-53250400	Weak transcription	Psoas Muscle	Psoas
2	chr20:53236200-53250400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr20:53241400-53248200	Weak transcription	NHDF-Ad	bronchial
4	chr20:53241400-53249800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr20:53242200-53249000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr20:53242400-53248200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr20:53242400-53248800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr20:53242400-53249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
9	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr20:53243000-53249600	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr20:53243000-53249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
12	chr20:53244600-53249600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr20:53244600-53249800	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr20:53246000-53248000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr20:53246200-53248200	Enhancers	Fetal Brain Female	brain
16	chr20:53246400-53249800	Weak transcription	Brain Germinal Matrix	brain
17	chr20:53246600-53251000	Enhancers	Fetal Brain Male	brain
18	chr20:53246800-53250000	Weak transcription	Fetal Muscle Leg	muscle

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