Variant report

Variant	rs5024811
Chromosome Location	chr6:150246034-150246035
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150155818..150157641-chr6:150245238..150247988,3	MCF-7	breast:
2	chr6:150181490..150187274-chr6:150243970..150248410,8	MCF-7	breast:
3	chr6:150208849..150210452-chr6:150245274..150246868,2	MCF-7	breast:
4	chr6:150044112..150046636-chr6:150245149..150247881,2	MCF-7	breast:
5	chr6:150243800..150245856-chr6:150245979..150247636,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000203722	Chromatin interaction
ENSG00000120256	Chromatin interaction
ENSG00000268592	Chromatin interaction

Extended variants
information (count: 38 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10457852	0.94[CEU][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.91[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12204653	0.94[CEU][hapmap];0.88[CHB][hapmap];0.84[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12209310	0.85[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12210822	0.94[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12527391	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs12528243	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1855572	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1999632	0.89[CEU][hapmap];0.84[JPT][hapmap];0.83[MEX][hapmap];0.86[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1999633	0.83[CEU][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2342766	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs3798763	0.94[CEU][hapmap];0.89[CHB][hapmap];0.92[CHD][hapmap];0.83[GIH][hapmap];0.89[JPT][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3922946	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3922947	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4473864	0.92[ASN][1000 genomes]
rs4869755	0.94[CEU][hapmap];0.89[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869756	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4869767	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4869768	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870078	0.94[CEU][hapmap];0.83[CHD][hapmap];0.80[JPT][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4870110	0.92[ASN][1000 genomes]
rs4870117	0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4870118	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57894361	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6557165	0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.94[JPT][hapmap];0.84[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6912330	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6914185	0.83[ASN][1000 genomes]
rs6925151	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7452592	0.83[EUR][1000 genomes]
rs7764677	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs915140	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9322229	0.94[CEU][hapmap];0.89[CHB][hapmap];0.93[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9371228	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9383941	0.85[ASW][hapmap];0.94[CEU][hapmap];0.89[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.94[JPT][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9397070	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[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	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv886765	chr6:150198491-150288722	Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Weak transcription Active TSS ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	esv1817805	chr6:150209592-150268708	Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Weak transcription ZNF genes & repeats Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs5024811	LATS1	cis	cerebellum	SCAN
rs5024811	RAET1G	cis	Thyroid	GTEx
rs5024811	RP11-350J20.5	cis	lung	GTEx
rs5024811	NUP43	cis	multi-tissue	Pritchard
rs5024811	RP11-350J20.9	cis	Esophagus Mucosa	GTEx
rs5024811	LRP11	cis	cerebellum	SCAN
rs5024811	LRP11	cis	parietal	SCAN
rs5024811	RP11-350J20.5	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150242800-150247800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
2	chr6:150244000-150246200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr6:150244200-150246800	Enhancers	Spleen	Spleen
4	chr6:150244800-150246200	Weak transcription	NHLF	lung
5	chr6:150244800-150246400	Weak transcription	Liver	Liver
6	chr6:150244800-150246400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
7	chr6:150244800-150246400	Weak transcription	Right Ventricle	heart
8	chr6:150244800-150246400	Weak transcription	HUVEC	blood vessel
9	chr6:150244800-150246400	Weak transcription	NHEK	skin
10	chr6:150244800-150246600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr6:150244800-150246600	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr6:150244800-150246600	Weak transcription	Brain Angular Gyrus	brain
13	chr6:150244800-150246600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr6:150244800-150246600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
15	chr6:150244800-150246800	Weak transcription	Aorta	Aorta
16	chr6:150244800-150246800	Weak transcription	Gastric	stomach
17	chr6:150244800-150246800	Weak transcription	Lung	lung
18	chr6:150244800-150246800	Weak transcription	HSMM	muscle
19	chr6:150244800-150246800	Weak transcription	HSMMtube	muscle
20	chr6:150244800-150247000	Weak transcription	A549	lung
21	chr6:150244800-150247000	Weak transcription	Hela-S3	cervix
22	chr6:150245000-150246200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr6:150245000-150246200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr6:150245000-150246200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr6:150245000-150246200	Weak transcription	Pancreas	Pancrea
26	chr6:150245000-150246200	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr6:150245000-150246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr6:150245000-150246400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
29	chr6:150245000-150246400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr6:150245000-150246400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr6:150245000-150246400	Weak transcription	Ovary	ovary
32	chr6:150245000-150246400	Weak transcription	Right Atrium	heart
33	chr6:150245000-150246400	Weak transcription	HMEC	breast
34	chr6:150245000-150246400	Weak transcription	Osteobl	bone
35	chr6:150245000-150246600	Weak transcription	Brain Hippocampus Middle	brain
36	chr6:150245600-150246400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
37	chr6:150245800-150246200	Bivalent Enhancer	HepG2	liver
38	chr6:150246000-150246400	Enhancers	Adipose Nuclei	Adipose
39	chr6:150246000-150246400	Bivalent Enhancer	Duodenum Mucosa	Duodenum
40	chr6:150246000-150246400	Enhancers	NHDF-Ad	bronchial
41	chr6:150246000-150246600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr6:150246000-150246600	Enhancers	Esophagus	oesophagus
43	chr6:150246000-150246600	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
44	chr6:150246000-150246600	Bivalent Enhancer	Fetal Intestine Small	intestine
45	chr6:150246000-150246600	Enhancers	Left Ventricle	heart
46	chr6:150246000-150246800	Bivalent Enhancer	Foreskin Melanocyte Primary Cells skin01	Skin
47	chr6:150246000-150246800	Bivalent Enhancer	Stomach Mucosa	stomach

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