Variant report

Variant	rs6098129
Chromosome Location	chr20:53248850-53248851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:52823919..52824500-chr20:53248272..53248952,2	MCF-7	breast:
2	chr20:52824443..52826039-chr20:53246176..53249112,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000101132	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10154005	0.87[CEU][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs13433172	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16999757	1.00[CHD][hapmap]
rs16999893	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs55705559	0.88[AMR][1000 genomes]
rs56138015	0.88[AMR][1000 genomes]
rs56187828	0.86[EUR][1000 genomes]
rs56294816	0.84[AMR][1000 genomes]
rs57120787	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6014087	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6014089	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014091	0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6014092	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6014098	0.87[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023385	1.00[CHD][hapmap]
rs6023422	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6023431	1.00[MEX][hapmap]
rs6023432	0.81[ASW][hapmap];0.88[LWK][hapmap];0.97[MKK][hapmap];0.90[TSI][hapmap];0.84[YRI][hapmap];0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6091933	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6091938	1.00[CHD][hapmap]
rs6091939	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6098104	0.84[AMR][1000 genomes]
rs6098111	0.85[AMR][1000 genomes]
rs6098116	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6098118	0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6098123	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6098130	0.87[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs68183459	0.80[EUR][1000 genomes]
rs7268501	1.00[CHD][hapmap]
rs73144055	0.82[AMR][1000 genomes]
rs73144063	0.88[AMR][1000 genomes]
rs73144072	0.81[AMR][1000 genomes]
rs73144079	0.84[AMR][1000 genomes]
rs73144086	0.88[AMR][1000 genomes]
rs73146053	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73146055	0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs73146076	0.80[EUR][1000 genomes]
rs8125542	1.00[CHD][hapmap]

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:16 , 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	chr20:53241400-53249800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr20:53242200-53249000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr20:53242400-53249800	Weak transcription	HUES64 Cell Line	embryonic stem cell
6	chr20:53242400-53270200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr20:53243000-53249600	Weak transcription	Cortex derived primary cultured neurospheres	brain
8	chr20:53243000-53249600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr20:53244600-53249600	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr20:53244600-53249800	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr20:53246400-53249800	Weak transcription	Brain Germinal Matrix	brain
12	chr20:53246600-53251000	Enhancers	Fetal Brain Male	brain
13	chr20:53246800-53250000	Weak transcription	Fetal Muscle Leg	muscle
14	chr20:53248200-53249800	Weak transcription	Fetal Brain Female	brain
15	chr20:53248800-53249200	Enhancers	iPS-20b Cell Line	embryonic stem cell
16	chr20:53248800-53250400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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