Variant report

Variant	rs10499219
Chromosome Location	chr6:140373746-140373747
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:140373569..140374771-chr6:140762117..140763007,5	MCF-7	breast:

Extended variants
information (count: 43 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10499216	0.98[ASN][1000 genomes]
rs1113096	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11966793	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs11967431	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11969633	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12523886	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12525793	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12526277	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12528420	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12529701	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12529920	0.86[EUR][1000 genomes]
rs1390500	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1496114	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17069706	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17069710	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17069727	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17069741	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17069805	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17069893	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1879097	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2050716	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2328026	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs57789174	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs59447713	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs60747543	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62429521	0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs62429525	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62431062	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62431064	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62431065	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62431066	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62431098	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431099	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431110	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62431142	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6915764	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs732015	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs73571530	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7770431	0.87[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869066	chr6:139777114-140639695	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	26 gene(s)	inside rSNPs	diseases
2	nsv1016532	chr6:140174639-141029988	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases
3	nsv1019508	chr6:140317472-140434466	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1022987	chr6:140344229-140463916	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:140365600-140374200	Weak transcription	A549	lung
2	chr6:140369400-140374600	Enhancers	Hela-S3	cervix
3	chr6:140370200-140373800	Enhancers	Fetal Heart	heart
4	chr6:140370600-140374800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr6:140370600-140375400	Enhancers	Muscle Satellite Cultured Cells	--
6	chr6:140370800-140373800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr6:140370800-140374800	Enhancers	Placenta Amnion	Placenta Amnion
8	chr6:140370800-140375000	Enhancers	NH-A	brain
9	chr6:140371200-140374000	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr6:140371200-140374600	Enhancers	Fetal Brain Male	brain
11	chr6:140371200-140374600	Enhancers	Osteobl	bone
12	chr6:140371400-140374800	Enhancers	HMEC	breast
13	chr6:140371400-140374800	Enhancers	NHEK	skin
14	chr6:140371400-140374800	Enhancers	NHLF	lung
15	chr6:140371400-140375000	Enhancers	NHDF-Ad	bronchial
16	chr6:140371600-140374600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr6:140371600-140375400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr6:140371600-140379400	Weak transcription	Placenta	Placenta
19	chr6:140371800-140374000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
20	chr6:140372200-140373800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:140372200-140375200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:140372400-140375000	Enhancers	Brain Germinal Matrix	brain
23	chr6:140372800-140373800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr6:140372800-140374200	Enhancers	Cortex derived primary cultured neurospheres	brain
25	chr6:140372800-140374200	Enhancers	Fetal Brain Female	brain
26	chr6:140372800-140374400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr6:140372800-140375000	Enhancers	Breast Myoepithelial Primary Cells	Breast
28	chr6:140373000-140374800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr6:140373000-140375000	Enhancers	Fetal Intestine Small	intestine
30	chr6:140373200-140374200	Enhancers	Fetal Stomach	stomach
31	chr6:140373200-140374800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr6:140373400-140374000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:140373600-140373800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr6:140373600-140374200	Enhancers	Left Ventricle	heart
35	chr6:140373600-140375200	Enhancers	Liver	Liver
36	chr6:140373600-140381000	Weak transcription	HSMM	muscle
37	chr6:140373600-140384200	Weak transcription	Pancreatic Islets	Pancreatic Islet

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