Variant report

Variant	rs6048615
Chromosome Location	chr20:23209414-23209415
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr20:23028507..23030914-chr20:23206513..23209479,3	MCF-7	breast:
2	chr20:23206231..23209945-chr20:23213936..23217641,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000178726	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1005856	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1099456	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11696272	0.96[CEU][hapmap];0.80[CHB][hapmap];0.91[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1338942	0.96[CHB][hapmap];0.96[JPT][hapmap];0.90[ASN][1000 genomes]
rs1338944	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1416399	0.99[ASN][1000 genomes]
rs1538445	0.80[EUR][1000 genomes]
rs1538446	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1572707	0.97[ASN][1000 genomes]
rs1856470	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2024897	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6036338	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048590	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6048591	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6048592	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048595	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6048612	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6048618	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6048619	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6076038	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6076039	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6076041	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs6083030	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083032	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6083033	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083036	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6083038	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6083042	0.96[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs6083043	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6106616	0.80[EUR][1000 genomes]
rs6113992	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6132576	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6132577	0.93[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6132578	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6132579	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62206882	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs750652	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8118328	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844924	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs844929	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs844930	0.88[ASN][1000 genomes]
rs844932	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844934	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs844936	0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844937	0.96[CEU][hapmap];0.95[CHB][hapmap];0.96[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844938	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844939	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844940	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844941	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs844942	0.96[CEU][hapmap];0.96[CHB][hapmap];0.96[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs867909	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs870225	0.92[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][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	nsv912817	chr20:23127661-23240969	Flanking Active TSS Weak transcription Bivalent Enhancer Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
2	nsv1066734	chr20:23170094-23277628	Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Bivalent/Poised TSS Strong transcription	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:23205400-23209800	Enhancers	Placenta	Placenta
2	chr20:23205400-23211400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr20:23205600-23212800	Enhancers	NHDF-Ad	bronchial
4	chr20:23205600-23213000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr20:23205800-23210400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr20:23206200-23213000	Enhancers	Osteobl	bone
7	chr20:23207400-23211600	Weak transcription	Hela-S3	cervix
8	chr20:23208200-23210000	Enhancers	Fetal Stomach	stomach
9	chr20:23208200-23211600	Weak transcription	Monocytes-CD14+_RO01746	blood
10	chr20:23208400-23211200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr20:23208400-23211400	Weak transcription	Lung	lung
12	chr20:23208400-23212200	Weak transcription	HUVEC	blood vessel
13	chr20:23208600-23210000	Enhancers	Stomach Mucosa	stomach
14	chr20:23208600-23210400	Enhancers	HSMMtube	muscle
15	chr20:23209000-23209600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr20:23209000-23210200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr20:23209000-23210400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr20:23209200-23209600	Enhancers	NH-A	brain
19	chr20:23209200-23209800	Enhancers	Fetal Muscle Leg	muscle
20	chr20:23209200-23209800	Enhancers	Right Atrium	heart
21	chr20:23209200-23209800	Enhancers	Stomach Smooth Muscle	stomach
22	chr20:23209200-23210000	Enhancers	HSMM	muscle
23	chr20:23209200-23210200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr20:23209200-23210200	Enhancers	Colon Smooth Muscle	Colon
25	chr20:23209200-23212800	Enhancers	NHLF	lung
26	chr20:23209400-23209800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr20:23209400-23209800	Enhancers	Ovary	ovary
28	chr20:23209400-23210000	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr20:23209400-23212200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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