Variant report

Variant	rs28475221
Chromosome Location	chr9:137002665-137002666
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:136999899-137003166	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:137001481-137002982	SK-N-MC	brain:	n/a	n/a

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr21:41236712..41238651-chr9:137001241..137003469,2	MCF-7	breast:
2	chr2:220091886..220094259-chr9:137000513..137003179,2	MCF-7	breast:
3	chr9:137001719..137003383-chr9:137240683..137243460,2	MCF-7	breast:
4	chr9:136930118..136934023-chr9:136998387..137002829,10	K562	blood:
5	chr9:137001564..137003951-chr9:137325246..137326831,2	MCF-7	breast:
6	chr9:136931194..136934944-chr9:136998387..137002829,6	K562	blood:
7	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
8	chr9:136930108..136935337-chr9:136999374..137002737,14	MCF-7	breast:
9	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
10	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
11	chr9:136888792..136891646-chr9:137000403..137003499,3	MCF-7	breast:
12	chr9:137000635..137002837-chr9:137296498..137299052,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000273249	TF binding region
WDR5	TF binding region
ENSG00000198925	Chromatin interaction
ENSG00000235106	Chromatin interaction
ENSG00000169925	Chromatin interaction
ENSG00000186350	Chromatin interaction
ENSG00000221676	Chromatin interaction

Extended variants
information (count: 46 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1128044	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11556390	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28410119	0.85[ASN][1000 genomes]
rs28412218	0.95[ASN][1000 genomes]
rs28415637	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28428662	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28438574	0.98[ASN][1000 genomes]
rs28473092	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28485659	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28490920	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28498266	0.88[AFR][1000 genomes]
rs28508246	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28522840	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28549758	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28567437	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28588875	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28604373	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28610236	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28611335	0.93[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs28635910	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28637447	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28647893	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28648812	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28661406	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28681320	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28681533	0.90[AFR][1000 genomes]
rs28695913	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28705801	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs34417824	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35401074	0.87[ASN][1000 genomes]
rs35715743	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35949820	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs36185416	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4358859	0.81[EUR][1000 genomes]
rs4744560	0.81[EUR][1000 genomes]
rs55874211	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7847227	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv894138	chr9:136839840-137093168	Strong transcription Genic enhancers Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Weak transcription Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
2	nsv825148	chr9:136848471-137025632	Flanking Bivalent TSS/Enh Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
3	nsv1048571	chr9:136872166-137265444	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
4	nsv894148	chr9:136874066-137093168	Enhancers Strong transcription Weak transcription Bivalent/Poised TSS ZNF genes & repeats Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv894151	chr9:136887757-137397609	Weak transcription Active TSS Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
6	nsv6751	chr9:136967475-137007131	Active TSS Flanking Active TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv894155	chr9:136969689-137364866	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	43 gene(s)	inside rSNPs	diseases
8	esv1793302	chr9:136990615-137390602	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
9	esv3392543	chr9:137000156-137002904	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:137000200-137002800	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr9:137000200-137003200	Active TSS	iPS-15b Cell Line	embryonic stem cell
3	chr9:137000400-137002800	Active TSS	iPS-20b Cell Line	embryonic stem cell
4	chr9:137001600-137003000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr9:137001600-137003000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
6	chr9:137001600-137004600	Flanking Active TSS	Stomach Smooth Muscle	stomach
7	chr9:137001800-137002800	Flanking Active TSS	Brain Germinal Matrix	brain
8	chr9:137001800-137003000	Flanking Active TSS	Brain Cingulate Gyrus	brain
9	chr9:137001800-137003200	Flanking Active TSS	Liver	Liver
10	chr9:137001800-137003800	Flanking Active TSS	Duodenum Mucosa	Duodenum
11	chr9:137001800-137004400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr9:137002000-137002800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr9:137002000-137002800	Flanking Active TSS	Brain Hippocampus Middle	brain
14	chr9:137002000-137003000	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:137002000-137003200	Flanking Active TSS	Hela-S3	cervix
16	chr9:137002000-137003400	Flanking Active TSS	Dnd41	blood
17	chr9:137002000-137004800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
18	chr9:137002200-137002800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr9:137002200-137002800	Flanking Active TSS	Colon Smooth Muscle	Colon
20	chr9:137002200-137003000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr9:137002200-137003200	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr9:137002200-137003400	Enhancers	Spleen	Spleen
23	chr9:137002200-137004200	Enhancers	Fetal Heart	heart
24	chr9:137002200-137004400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
25	chr9:137002400-137002800	Enhancers	Primary T cells from cord blood	blood
26	chr9:137002400-137002800	Enhancers	Psoas Muscle	Psoas
27	chr9:137002400-137002800	Transcr. at gene 5' and 3'	A549	lung
28	chr9:137002400-137003000	Enhancers	GM12878-XiMat	blood
29	chr9:137002400-137003200	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr9:137002400-137003200	Enhancers	HSMMtube	muscle
31	chr9:137002400-137003400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:137002400-137003400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
33	chr9:137002400-137003400	Enhancers	Brain Anterior Caudate	brain
34	chr9:137002400-137003400	Weak transcription	Fetal Kidney	kidney
35	chr9:137002400-137003400	Enhancers	Rectal Mucosa Donor 29	rectum
36	chr9:137002400-137003600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
37	chr9:137002400-137003600	Weak transcription	Aorta	Aorta
38	chr9:137002400-137003600	Enhancers	Fetal Lung	lung
39	chr9:137002400-137003800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr9:137002400-137003800	Enhancers	Primary monocytes fromperipheralblood	blood
41	chr9:137002400-137003800	Enhancers	Primary B cells from peripheral blood	blood
42	chr9:137002400-137003800	Enhancers	Fetal Brain Male	brain
43	chr9:137002400-137003800	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr9:137002400-137003800	Enhancers	Placenta	Placenta
45	chr9:137002400-137003800	Enhancers	Fetal Thymus	thymus
46	chr9:137002400-137003800	Enhancers	Stomach Mucosa	stomach
47	chr9:137002400-137003800	Flanking Active TSS	HepG2	liver
48	chr9:137002400-137004000	Enhancers	Primary T helper cells fromperipheralblood	blood
49	chr9:137002400-137004200	Enhancers	Gastric	stomach
50	chr9:137002400-137004200	Enhancers	Lung	lung

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