Variant report

Variant	rs7263678
Chromosome Location	chr20:53244727-53244728
allele	C/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	chr20:52823764..52827525-chr20:53242142..53245789,3	MCF-7	breast:
3	chr20:53241214..53243048-chr20:53243529..53246350,2	MCF-7	breast:
4	chr20:53229800..53233428-chr20:53242430..53245775,3	MCF-7	breast:
5	chr20:53228713..53231762-chr20:53243717..53245760,3	K562	blood:
6	chr20:53216884..53218583-chr20:53242358..53245135,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 78 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs13040265	1.00[CHD][hapmap]
rs1569985	1.00[CHD][hapmap]
rs16999872	1.00[ASN][1000 genomes]
rs1983702	1.00[CHD][hapmap]
rs2180462	1.00[CHD][hapmap]
rs2208074	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2208075	1.00[CHD][hapmap]
rs2224269	1.00[CHD][hapmap]
rs28663252	1.00[ASN][1000 genomes]
rs2870331	1.00[ASN][1000 genomes]
rs2870332	1.00[ASN][1000 genomes]
rs2870333	1.00[CHD][hapmap]
rs2870337	1.00[CHD][hapmap]
rs2904386	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4302265	1.00[CHD][hapmap]
rs4324376	1.00[ASN][1000 genomes]
rs4334548	1.00[CHD][hapmap]
rs4542911	1.00[ASN][1000 genomes]
rs4581960	1.00[ASN][1000 genomes]
rs4809968	1.00[ASN][1000 genomes]
rs4809969	1.00[CHD][hapmap]
rs4811510	1.00[ASN][1000 genomes]
rs4811511	1.00[ASN][1000 genomes]
rs4811513	0.83[EUR][1000 genomes];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]
rs6014081	0.89[CEU][hapmap];1.00[CHD][hapmap]
rs6014094	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014096	0.92[CEU][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6014106	1.00[CHD][hapmap]
rs6023367	1.00[CHD][hapmap]
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[CHD][hapmap];1.00[ASN][1000 genomes]
rs6023407	0.88[CEU][hapmap]
rs6023408	1.00[ASN][1000 genomes]
rs6023409	1.00[ASN][1000 genomes]
rs6023410	1.00[ASN][1000 genomes]
rs6023423	0.85[CEU][hapmap];1.00[CHD][hapmap];0.81[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6023428	1.00[CEU][hapmap];0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023429	1.00[CEU][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6023430	0.94[ASW][hapmap];1.00[CHD][hapmap];0.88[MEX][hapmap];0.82[MKK][hapmap];0.81[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs6023474	1.00[CHD][hapmap]
rs6064093	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6064102	1.00[CHD][hapmap]
rs6068916	1.00[ASN][1000 genomes]
rs6068920	1.00[ASN][1000 genomes]
rs6068924	1.00[CHD][hapmap]
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	1.00[CHD][hapmap];1.00[ASN][1000 genomes]
rs6098120	1.00[ASN][1000 genomes]
rs6098124	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6098158	1.00[CHD][hapmap]
rs6123404	1.00[CHD][hapmap]
rs7261209	1.00[ASN][1000 genomes]
rs7263680	1.00[ASN][1000 genomes]
rs7269966	1.00[ASN][1000 genomes]
rs7270451	1.00[CHD][hapmap];0.83[MEX][hapmap]
rs7270971	1.00[CHD][hapmap]
rs8115071	1.00[CHD][hapmap]
rs8124702	1.00[CHD][hapmap]
rs910850	1.00[CHD][hapmap]
rs967377	1.00[CHD][hapmap];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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7263678	CSTF1	cis	cerebellum	SCAN
rs7263678	PMEPA1	cis	parietal	SCAN

Chromatin state (count:19 , 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	chr20:53240800-53245800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr20:53241000-53246200	Weak transcription	Skeletal Muscle Female	skeletal muscle
5	chr20:53241400-53248200	Weak transcription	NHDF-Ad	bronchial
6	chr20:53241400-53249800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr20:53241800-53245800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr20:53242200-53245800	Enhancers	Fetal Brain Male	brain
9	chr20:53242200-53249000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr20:53242400-53248200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:53242400-53248800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
12	chr20:53242400-53249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
13	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr20:53243000-53249600	Weak transcription	Cortex derived primary cultured neurospheres	brain
15	chr20:53243000-53249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr20:53243400-53245600	Weak transcription	Brain Germinal Matrix	brain
17	chr20:53243800-53246200	Weak transcription	Fetal Brain Female	brain
18	chr20:53244600-53249600	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr20:53244600-53249800	Weak transcription	H9 Cell Line	embryonic stem cell

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