Variant report

Variant	rs6824893
Chromosome Location	chr4:57372243-57372244
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	chr4:57371959..57374819-chr4:57375390..57378214,2	MCF-7	breast:

Extended variants
information (count: 53 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10051	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10434444	0.80[ASN][1000 genomes]
rs1060472	0.80[ASN][1000 genomes]
rs11133442	0.86[ASN][1000 genomes]
rs12501334	0.80[ASN][1000 genomes]
rs12503412	0.80[ASN][1000 genomes]
rs12505767	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12505939	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12508008	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12509542	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12510712	0.82[ASN][1000 genomes]
rs12511770	0.88[ASN][1000 genomes]
rs12513091	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12646890	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs14211	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1474179	0.89[ASN][1000 genomes]
rs17086794	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17086832	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17086853	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1967559	0.86[ASN][1000 genomes]
rs1983378	0.80[ASN][1000 genomes]
rs2030366	0.80[ASN][1000 genomes]
rs28866881	0.80[ASN][1000 genomes]
rs4340842	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4346704	0.88[ASN][1000 genomes]
rs4618376	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4864583	0.80[ASN][1000 genomes]
rs4864585	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4865092	0.81[ASN][1000 genomes]
rs4865103	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4865107	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4865108	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs55915354	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56040009	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56099714	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56229630	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56392224	0.80[ASN][1000 genomes]
rs56887793	0.81[ASN][1000 genomes]
rs58333131	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6554358	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs66858948	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66863699	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6820314	0.80[ASN][1000 genomes]
rs6821301	0.91[ASN][1000 genomes]
rs6829250	0.80[ASN][1000 genomes]
rs6834696	0.82[ASN][1000 genomes]
rs6849183	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7664841	0.91[ASN][1000 genomes]

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	nsv999639	chr4:56942917-57401310	Weak transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv1014045	chr4:56942917-57404511	Weak transcription Strong transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv868815	chr4:57114268-58084688	Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	88 gene(s)	inside rSNPs	diseases
4	nsv530121	chr4:57167367-57695576	Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	59 gene(s)	inside rSNPs	diseases
5	nsv829941	chr4:57359551-57553136	Weak transcription Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs6824893	PPAT	Cis_1M	lymphoblastoid	RTeQTL
rs6824893	SRP72	cis	Esophagus Mucosa	GTEx
rs6824893	SRP72	Cis_1M	lymphoblastoid	RTeQTL
rs6824893	SRP72	cis	Adipose Subcutaneous	GTEx
rs6824893	SRP72	cis	Whole Blood	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:57370200-57373000	Weak transcription	Dnd41	blood
2	chr4:57370200-57377400	Weak transcription	K562	blood
3	chr4:57371000-57372600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
4	chr4:57371200-57372400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr4:57371200-57372400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr4:57371200-57373000	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr4:57371200-57373000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
8	chr4:57371200-57373000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr4:57371400-57372400	Active TSS	H9 Cell Line	embryonic stem cell
10	chr4:57371400-57372400	Active TSS	Breast Myoepithelial Primary Cells	Breast
11	chr4:57371400-57372400	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
12	chr4:57371400-57372400	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
13	chr4:57371400-57372400	Active TSS	Aorta	Aorta
14	chr4:57371400-57372400	Flanking Active TSS	Liver	Liver
15	chr4:57371400-57372400	Active TSS	Brain Cingulate Gyrus	brain
16	chr4:57371400-57372400	Flanking Active TSS	Fetal Intestine Small	intestine
17	chr4:57371400-57372400	Active TSS	Ovary	ovary
18	chr4:57371400-57372400	Flanking Active TSS	Pancreas	Pancrea
19	chr4:57371400-57372400	Active TSS	Stomach Mucosa	stomach
20	chr4:57371400-57372400	Active TSS	HSMMtube	muscle
21	chr4:57371400-57372600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
22	chr4:57371400-57372600	Flanking Bivalent TSS/Enh	Primary neutrophils fromperipheralblood	blood
23	chr4:57371400-57372600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr4:57371400-57372600	Flanking Active TSS	Right Ventricle	heart
25	chr4:57371400-57372600	Flanking Active TSS	HMEC	breast
26	chr4:57371400-57372600	Active TSS	NHDF-Ad	bronchial
27	chr4:57371400-57372800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell
28	chr4:57371400-57372800	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr4:57371400-57372800	Flanking Active TSS	Primary B cells from peripheral blood	blood
30	chr4:57371400-57372800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
31	chr4:57371400-57372800	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr4:57371400-57372800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
33	chr4:57371400-57372800	Active TSS	Brain Angular Gyrus	brain
34	chr4:57371400-57372800	Active TSS	Brain Substantia Nigra	brain
35	chr4:57371400-57372800	Active TSS	Fetal Kidney	kidney
36	chr4:57371400-57372800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
37	chr4:57371400-57372800	Flanking Active TSS	Thymus	Thymus
38	chr4:57371400-57372800	Flanking Active TSS	NHEK	skin
39	chr4:57371400-57373000	Flanking Active TSS	Primary hematopoietic stem cells	blood
40	chr4:57371400-57373000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr4:57371400-57373000	Flanking Active TSS	Duodenum Mucosa	Duodenum
42	chr4:57371400-57373000	Active TSS	Duodenum Smooth Muscle	Duodenum
43	chr4:57371400-57373000	Active TSS	Pancreatic Islets	Pancreatic Islet
44	chr4:57371400-57373000	Flanking Active TSS	HUVEC	blood vessel
45	chr4:57371400-57373200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
46	chr4:57371600-57372400	Active TSS	Brain Germinal Matrix	brain
47	chr4:57371600-57372400	Active TSS	Colon Smooth Muscle	Colon
48	chr4:57371600-57372400	Active TSS	Fetal Brain Female	brain
49	chr4:57371600-57372400	Active TSS	Spleen	Spleen
50	chr4:57371600-57372400	Active TSS	NH-A	brain

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