Variant report

Variant	rs73831577
Chromosome Location	chr3:48543758-48543759
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr3:48543527-48544098	PBDE	blood:	n/a	chr3:48543699-48543706 chr3:48543699-48543706 chr3:48543698-48543708 chr3:48543699-48543708 chr3:48543700-48543717 chr3:48543699-48543706 chr3:48543692-48543713 chr3:48543697-48543709 chr3:48543699-48543708
2	POLR2A	chr3:48543661-48543834	GM12878	blood:	n/a	n/a
3	POLR2A	chr3:48543528-48543862	U87	brain:	n/a	n/a
4	POLR2A	chr3:48543528-48543838	U87	brain:	n/a	n/a
5	POLR2A	chr3:48543295-48545715	U87	brain:	n/a	n/a
6	POLR2A	chr3:48543140-48545709	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr3:48486835..48489928-chr3:48540255..48543800,6	MCF-7	breast:
2	chr3:48541156..48543765-chr3:48670075..48672910,2	K562	blood:
3	chr3:48542816..48545156-chr3:48545848..48548841,2	K562	blood:
4	chr3:48506093..48508712-chr3:48542619..48544256,2	K562	blood:
5	chr3:48504031..48516338-chr3:48532689..48546353,31	MCF-7	breast:
6	chr3:48486688..48489552-chr3:48542310..48546358,4	K562	blood:
7	chr3:48512656..48514553-chr3:48541410..48544214,2	K562	blood:

Variant related genes	Relation type
SHISA5	TF binding region
ENSG00000164054	Chromatin interaction
ENSG00000225697	Chromatin interaction
ENSG00000244380	Chromatin interaction
ENSG00000213689	Chromatin interaction
ENSG00000164053	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10780032	1.00[EUR][1000 genomes]
rs11130169	1.00[EUR][1000 genomes]
rs11915428	1.00[EUR][1000 genomes]
rs13062723	1.00[AMR][1000 genomes]
rs3924179	1.00[EUR][1000 genomes]
rs4858818	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs55782175	1.00[EUR][1000 genomes]
rs58708931	1.00[EUR][1000 genomes]
rs58835493	1.00[EUR][1000 genomes]
rs59352296	1.00[EUR][1000 genomes]
rs60352528	1.00[EUR][1000 genomes]
rs6442122	1.00[EUR][1000 genomes]
rs6791777	1.00[EUR][1000 genomes]
rs6793732	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6801348	1.00[EUR][1000 genomes]
rs73830466	1.00[EUR][1000 genomes]
rs73830478	1.00[EUR][1000 genomes]
rs73831565	1.00[EUR][1000 genomes]
rs73831572	1.00[EUR][1000 genomes]
rs73831579	1.00[EUR][1000 genomes]
rs7633433	1.00[EUR][1000 genomes]
rs898226	1.00[EUR][1000 genomes]
rs9852211	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9860187	1.00[EUR][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	nsv834684	chr3:48385699-48589323	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv590242	chr3:48433635-48556339	Strong transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
3	esv1802114	chr3:48498822-48577670	Strong transcription Weak transcription Genic enhancers Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
4	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
5	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48542200-48545200	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
2	chr3:48542200-48545600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr3:48542400-48544800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr3:48542400-48544800	Weak transcription	Small Intestine	intestine
5	chr3:48542400-48544800	Enhancers	Hela-S3	cervix
6	chr3:48542400-48544800	Weak transcription	HSMMtube	muscle
7	chr3:48542400-48545600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr3:48542400-48545800	Enhancers	Primary T cells fromperipheralblood	blood
9	chr3:48542400-48545800	Enhancers	Primary T helper cells PMA-I stimulated	--
10	chr3:48542400-48545800	Enhancers	Placenta	Placenta
11	chr3:48542600-48544200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr3:48542600-48544200	Weak transcription	HMEC	breast
13	chr3:48542600-48544600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr3:48542600-48544600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:48542600-48544600	Weak transcription	Brain Substantia Nigra	brain
16	chr3:48542600-48544800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:48542600-48544800	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:48542600-48544800	Weak transcription	Brain Angular Gyrus	brain
19	chr3:48542600-48544800	Weak transcription	HSMM	muscle
20	chr3:48542600-48544800	Weak transcription	Osteobl	bone
21	chr3:48542600-48545200	Weak transcription	Colonic Mucosa	Colon
22	chr3:48542600-48545600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr3:48542600-48545600	Weak transcription	GM12878-XiMat	blood
24	chr3:48542600-48554800	Weak transcription	Fetal Brain Female	brain
25	chr3:48542800-48544200	Weak transcription	Primary T cells from cord blood	blood
26	chr3:48542800-48544200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr3:48542800-48544400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr3:48542800-48544600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr3:48542800-48544600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr3:48542800-48544600	Weak transcription	A549	lung
31	chr3:48542800-48544800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr3:48542800-48544800	Weak transcription	H9 Cell Line	embryonic stem cell
33	chr3:48542800-48544800	Weak transcription	HUES48 Cell Line	embryonic stem cell
34	chr3:48542800-48544800	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr3:48542800-48544800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr3:48542800-48544800	Weak transcription	Primary monocytes fromperipheralblood	blood
37	chr3:48542800-48544800	Weak transcription	Primary B cells from cord blood	blood
38	chr3:48542800-48544800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
39	chr3:48542800-48544800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr3:48542800-48544800	Weak transcription	Muscle Satellite Cultured Cells	--
41	chr3:48542800-48544800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
42	chr3:48542800-48544800	Weak transcription	Brain Cingulate Gyrus	brain
43	chr3:48542800-48544800	Weak transcription	Brain Hippocampus Middle	brain
44	chr3:48542800-48544800	Weak transcription	Gastric	stomach
45	chr3:48542800-48544800	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:48542800-48544800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr3:48542800-48544800	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr3:48542800-48544800	Weak transcription	NH-A	brain
49	chr3:48542800-48544800	Weak transcription	NHLF	lung
50	chr3:48542800-48545000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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