Variant report

Variant	rs6098009
Chromosome Location	chr20:53096616-53096617
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr20:52998265..52998905-chr20:53096241..53096887,2	MCF-7	breast:
2	chr20:53095482..53097034-chr20:53262598..53264162,9	MCF-7	breast:
3	chr20:53090363..53095555-chr20:53096070..53104073,10	MCF-7	breast:
4	chr20:53095873..53096821-chr20:53265191..53266014,2	MCF-7	breast:
5	chr20:53084969..53087855-chr20:53094880..53097639,2	MCF-7	breast:
6	chr20:53094793..53096626-chr20:53100134..53103148,3	MCF-7	breast:
7	chr20:53067433..53069648-chr20:53093856..53096720,2	MCF-7	breast:
8	chr20:53096009..53097873-chr20:53102491..53104173,2	MCF-7	breast:
9	chr20:52713294..52713893-chr20:53095867..53096825,2	MCF-7	breast:
10	chr20:53094603..53097316-chr20:53132108..53133984,2	MCF-7	breast:
11	chr20:53095947..53096812-chr20:53262655..53264011,3	MCF-7	breast:
12	chr20:53073105..53076272-chr20:53092801..53096708,6	MCF-7	breast:
13	chr20:52835947..52837988-chr20:53095859..53097037,10	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000101134	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs11907464	0.82[EUR][1000 genomes]
rs12329481	0.88[CEU][hapmap]
rs13040866	0.82[EUR][1000 genomes]
rs13042185	1.00[CEU][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13042986	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13044898	1.00[CEU][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes]
rs1330017	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16999643	0.88[CEU][hapmap]
rs2297153	0.87[ASN][1000 genomes]
rs34310366	0.97[EUR][1000 genomes]
rs34433522	0.92[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34502501	0.97[EUR][1000 genomes]
rs34616206	0.98[EUR][1000 genomes]
rs34683517	0.97[EUR][1000 genomes]
rs34803565	0.87[ASN][1000 genomes]
rs35269605	0.87[EUR][1000 genomes]
rs35276316	1.00[EUR][1000 genomes]
rs35321528	0.89[EUR][1000 genomes]
rs6014019	0.88[CEU][hapmap]
rs6014020	0.88[CEU][hapmap]
rs6014027	1.00[CEU][hapmap]
rs6014032	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.92[TSI][hapmap];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6023244	0.88[CEU][hapmap]
rs6023245	0.88[CEU][hapmap]
rs6023251	0.88[CEU][hapmap]
rs6023254	0.88[CEU][hapmap]
rs6023269	0.82[EUR][1000 genomes]
rs6023270	0.82[EUR][1000 genomes]
rs6023272	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023273	1.00[CEU][hapmap];0.87[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6023274	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6023275	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023276	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6023278	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs6023291	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.89[MEX][hapmap];0.92[TSI][hapmap];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6023295	0.87[ASN][1000 genomes]
rs6023307	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[YRI][hapmap];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6023309	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6023323	1.00[CHB][hapmap];0.85[TSI][hapmap];0.87[ASN][1000 genomes]
rs6091886	0.88[CEU][hapmap]
rs6091890	0.81[EUR][1000 genomes]
rs6091891	1.00[CEU][hapmap];1.00[GIH][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];1.00[EUR][1000 genomes]
rs6091895	0.87[ASN][1000 genomes]
rs6098005	0.84[EUR][1000 genomes]
rs6098006	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098007	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098008	1.00[CEU][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098011	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs66631852	0.87[EUR][1000 genomes]
rs67687183	0.97[EUR][1000 genomes]
rs922398	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 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	nsv834012	chr20:52921007-53097177	Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6098009	ZNF217	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53093400-53106400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr20:53093800-53099000	Weak transcription	Ovary	ovary
3	chr20:53094000-53111600	Weak transcription	Fetal Muscle Leg	muscle
4	chr20:53095600-53096800	Enhancers	HUES64 Cell Line	embryonic stem cell
5	chr20:53095600-53097200	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr20:53095800-53096800	Enhancers	HUES6 Cell Line	embryonic stem cell
7	chr20:53096000-53096800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr20:53096000-53097200	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr20:53096000-53097400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:53096200-53096800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr20:53096200-53103000	Weak transcription	Osteobl	bone
12	chr20:53096400-53097400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
13	chr20:53096600-53096800	Active TSS	Fetal Brain Male	brain
14	chr20:53096600-53098000	Weak transcription	Fetal Brain Female	brain
15	chr20:53096600-53099000	Weak transcription	H9 Cell Line	embryonic stem cell

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