Variant report

Variant	rs6098118
Chromosome Location	chr20:53231492-53231493
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr20:53227273..53231686-chr20:53235441..53239585,4	MCF-7	breast:
2	chr20:53229800..53233428-chr20:53242430..53245775,3	MCF-7	breast:
3	chr20:53228713..53231762-chr20:53243717..53245760,3	K562	blood:
4	chr20:53231134..53234154-chr20:53242124..53244306,3	MCF-7	breast:
5	chr20:53231002..53233053-chr20:53235777..53237656,2	MCF-7	breast:
6	chr20:53213011..53216451-chr20:53226919..53231866,4	MCF-7	breast:

Extended variants
information (count: 56 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs10154005	0.85[CEU][hapmap];0.94[TSI][hapmap];0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10485784	0.85[CEU][hapmap];1.00[GIH][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs13433172	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs16999893	0.85[CEU][hapmap]
rs17327539	0.84[EUR][1000 genomes]
rs28663252	0.86[EUR][1000 genomes]
rs55705559	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs55960128	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs56138015	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56187828	0.84[AMR][1000 genomes]
rs56294816	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56371656	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs57120787	0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6014059	1.00[GIH][hapmap]
rs6014087	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6014089	0.85[CEU][hapmap];0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6014098	0.85[CEU][hapmap]
rs6023244	1.00[GIH][hapmap]
rs6023245	1.00[GIH][hapmap]
rs6023251	1.00[GIH][hapmap]
rs6023382	0.82[CEU][hapmap];0.82[EUR][1000 genomes]
rs6023383	1.00[GIH][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes]
rs6023384	0.85[CEU][hapmap]
rs6023386	0.85[CEU][hapmap]
rs6023396	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6023422	0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6023431	0.83[TSI][hapmap]
rs6068930	1.00[GIH][hapmap]
rs6091886	1.00[GIH][hapmap]
rs6091925	0.85[CEU][hapmap]
rs6091933	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6091939	0.84[TSI][hapmap];0.88[AMR][1000 genomes]
rs6098093	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6098099	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.92[LWK][hapmap];0.88[MKK][hapmap];0.88[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs6098104	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6098111	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs6098116	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6098123	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6098129	0.84[TSI][hapmap];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6098130	0.85[CEU][hapmap];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs62214433	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs67907005	0.84[EUR][1000 genomes]
rs73140147	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73144055	0.93[AMR][1000 genomes]
rs73144063	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs73144072	0.87[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73144079	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73144086	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs73146053	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73146055	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs873078	1.00[GIH][hapmap]

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	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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:53204600-53240600	Weak transcription	Left Ventricle	heart
2	chr20:53215200-53236400	Weak transcription	Aorta	Aorta
3	chr20:53217000-53235800	Weak transcription	Brain Germinal Matrix	brain
4	chr20:53217400-53240600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr20:53221600-53239000	Weak transcription	Osteobl	bone
6	chr20:53227400-53232800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr20:53227400-53235600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr20:53227600-53235000	Weak transcription	Fetal Brain Male	brain
9	chr20:53227800-53233000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr20:53227800-53239000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:53229000-53235800	Weak transcription	Fetal Lung	lung
12	chr20:53229200-53234600	Weak transcription	Fetal Muscle Leg	muscle
13	chr20:53229200-53240600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr20:53230000-53233600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr20:53231400-53236000	Weak transcription	Fetal Brain Female	brain

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