Variant report

Variant	rs28408860
Chromosome Location	chr9:136999589-136999590
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:1)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:136999465-136999611	K562	blood:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr9:136930118..136934023-chr9:136998387..137002829,10	K562	blood:
2	chr9:136931194..136934944-chr9:136998387..137002829,6	K562	blood:
3	chr9:136999027..137003702-chr9:137026566..137032835,8	MCF-7	breast:
4	chr9:136930108..136935337-chr9:136999374..137002737,14	MCF-7	breast:
5	chr9:136997943..137000936-chr9:137029556..137031957,3	K562	blood:
6	chr9:136999035..137002778-chr9:137027888..137031331,5	K562	blood:
7	chr9:136282958..136284963-chr9:136998714..137001684,2	K562	blood:
8	chr9:136928987..136935981-chr9:136998799..137005312,16	MCF-7	breast:
9	chr9:136999192..137001560-chr9:137216028..137218729,4	MCF-7	breast:

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

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BRD3-1	chr9:136999207-137000046	XLOC_007882

No data

Variant related genes	Relation type
WDR5	TF binding region
ENSG00000221676	Chromatin interaction
ENSG00000186350	Chromatin interaction
ENSG00000148300	Chromatin interaction
ENSG00000169925	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs28401669	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28437234	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28463472	0.85[AMR][1000 genomes]
rs28473627	0.99[ASN][1000 genomes]
rs28549934	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs28580780	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28581991	0.88[ASN][1000 genomes]
rs28587783	0.84[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs28602914	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28616242	0.96[ASN][1000 genomes]
rs28759362	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:136994600-136999800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr9:136996400-136999600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr9:136996400-136999600	Weak transcription	Colon Smooth Muscle	Colon
4	chr9:136996400-136999600	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr9:136996600-136999600	Weak transcription	Fetal Intestine Small	intestine
6	chr9:136996600-136999600	Weak transcription	A549	lung
7	chr9:136996600-136999800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr9:136996600-136999800	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr9:136996600-136999800	Weak transcription	Duodenum Smooth Muscle	Duodenum
10	chr9:136996600-136999800	Weak transcription	Small Intestine	intestine
11	chr9:136996800-136999600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
12	chr9:136996800-136999600	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr9:136996800-136999600	Weak transcription	Rectal Smooth Muscle	rectum
14	chr9:136996800-136999800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr9:136996800-136999800	Weak transcription	Left Ventricle	heart
16	chr9:136997000-136999600	Weak transcription	Fetal Intestine Large	intestine
17	chr9:136997000-136999600	Weak transcription	Ovary	ovary
18	chr9:136997000-136999600	Weak transcription	Right Ventricle	heart
19	chr9:136997000-136999800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr9:136997000-136999800	Weak transcription	Psoas Muscle	Psoas
21	chr9:136997000-136999800	Weak transcription	Right Atrium	heart
22	chr9:136997000-137000000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr9:136997200-136999600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:136997200-136999800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr9:136997400-136999600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr9:136997400-136999600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:136997400-136999800	Weak transcription	HSMM	muscle
28	chr9:136997400-137000000	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr9:136997400-137000000	Weak transcription	HSMMtube	muscle
30	chr9:136997600-136999800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr9:136997800-136999800	Weak transcription	H1 Cell Line	embryonic stem cell
32	chr9:136997800-136999800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr9:136997800-136999800	Weak transcription	Gastric	stomach
34	chr9:136997800-137000000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr9:136998200-136999600	Weak transcription	Lung	lung
36	chr9:136998200-136999800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
37	chr9:136998600-136999800	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr9:136999000-136999600	Enhancers	Dnd41	blood
39	chr9:136999000-136999800	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr9:136999000-136999800	Enhancers	Fetal Muscle Leg	muscle
41	chr9:136999000-136999800	Enhancers	Skeletal Muscle Male	skeletal muscle
42	chr9:136999000-137000000	Enhancers	Primary monocytes fromperipheralblood	blood
43	chr9:136999200-136999600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr9:136999200-136999600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr9:136999200-136999600	Enhancers	HepG2	liver
46	chr9:136999200-136999600	Enhancers	Monocytes-CD14+_RO01746	blood
47	chr9:136999200-136999800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
48	chr9:136999200-136999800	Enhancers	HUES48 Cell Line	embryonic stem cell
49	chr9:136999200-136999800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
50	chr9:136999200-136999800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin

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