Variant report

Variant	rs6049829
Chromosome Location	chr20:24629040-24629041
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	chr20:24623933..24625636-chr20:24628321..24630040,2	MCF-7	breast:

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs6049828	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6049833	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049834	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6049835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs761438	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv9793	chr20:23939613-24734850	Bivalent Enhancer Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	esv3332519	chr20:24535099-24815615	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv912824	chr20:24612808-24639916	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

No data

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:24615400-24633800	Weak transcription	Pancreatic Islets	Pancreatic Islet
2	chr20:24616200-24639600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr20:24616400-24630200	Weak transcription	Brain Angular Gyrus	brain
4	chr20:24620000-24641200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr20:24625200-24630600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr20:24625600-24629400	Weak transcription	Osteobl	bone
7	chr20:24625600-24633800	Weak transcription	Spleen	Spleen
8	chr20:24626000-24629600	Enhancers	Fetal Thymus	thymus
9	chr20:24627000-24629400	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr20:24627400-24630200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr20:24628000-24633600	Enhancers	Fetal Brain Male	brain
12	chr20:24628400-24629400	Weak transcription	Fetal Brain Female	brain
13	chr20:24628600-24629200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr20:24628600-24629200	Enhancers	Right Atrium	heart
15	chr20:24628600-24629400	Enhancers	Brain Cingulate Gyrus	brain
16	chr20:24628600-24629400	Enhancers	Fetal Muscle Leg	muscle
17	chr20:24628600-24630800	Enhancers	Brain Substantia Nigra	brain
18	chr20:24628600-24631000	Enhancers	Brain Hippocampus Middle	brain
19	chr20:24628600-24631600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr20:24628600-24631800	Weak transcription	HMEC	breast
21	chr20:24628800-24629200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr20:24628800-24629400	Enhancers	Right Ventricle	heart
23	chr20:24628800-24630000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
24	chr20:24628800-24631000	Enhancers	Primary B cells from peripheral blood	blood
25	chr20:24629000-24629200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr20:24629000-24629200	Enhancers	Fetal Stomach	stomach
27	chr20:24629000-24630200	Weak transcription	Colon Smooth Muscle	Colon
28	chr20:24629000-24633600	Enhancers	NHLF	lung

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