Variant report

Variant	rs11142346
Chromosome Location	chr9:72871945-72871946
allele	C/G
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	POLR2A	chr9:72871907-72872109	HepG2	liver:	n/a	n/a
2	POLR2A	chr9:72870291-72877116	IMR90	lung:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:72726692..72728267-chr9:72871219..72873032,2	MCF-7	breast:
2	chr9:72871186..72872849-chr9:73028190..73030062,2	K562	blood:

Variant related genes	Relation type
SMC5	TF binding region
ENSG00000119138	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10868798	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1104709	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11142019	0.88[AMR][1000 genomes]
rs11142141	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11142355	0.88[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11791792	0.87[AMR][1000 genomes]
rs11793851	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11794396	0.93[AMR][1000 genomes]
rs1180085	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1180090	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1180093	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1180095	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1180109	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1180116	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1180131	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12005243	0.93[AMR][1000 genomes]
rs12338030	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343885	0.93[AMR][1000 genomes]
rs12346675	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12352944	0.93[AMR][1000 genomes]
rs12684881	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2148856	0.93[AMR][1000 genomes]
rs2183361	0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4507832	0.82[AMR][1000 genomes]
rs4744593	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs58704591	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62570306	0.87[AMR][1000 genomes]
rs62570318	1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62570323	0.82[AFR][1000 genomes]
rs7019433	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7023586	0.93[AMR][1000 genomes]
rs7028657	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs72712267	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72712271	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72712284	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7847861	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7868421	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7873075	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047862	chr9:72746875-73138287	Enhancers Strong transcription Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
2	nsv831615	chr9:72852705-73019692	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:72868000-72872600	Weak transcription	Brain Cingulate Gyrus	brain
2	chr9:72869600-72873600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
3	chr9:72869800-72873600	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr9:72870200-72872200	Enhancers	Dnd41	blood
5	chr9:72870200-72872800	Flanking Active TSS	Muscle Satellite Cultured Cells	--
6	chr9:72870400-72872000	Flanking Active TSS	HMEC	breast
7	chr9:72870400-72872200	Enhancers	Placenta Amnion	Placenta Amnion
8	chr9:72870400-72873000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr9:72870400-72873600	Flanking Active TSS	Osteobl	bone
10	chr9:72870400-72874800	Active TSS	Right Atrium	heart
11	chr9:72870600-72872400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr9:72870600-72872400	Active TSS	Rectal Mucosa Donor 29	rectum
13	chr9:72870600-72872800	Enhancers	Fetal Brain Female	brain
14	chr9:72870600-72875000	Active TSS	Aorta	Aorta
15	chr9:72870800-72872000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr9:72870800-72872000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
17	chr9:72870800-72872000	Flanking Active TSS	Stomach Smooth Muscle	stomach
18	chr9:72870800-72872000	Flanking Active TSS	NHEK	skin
19	chr9:72870800-72875200	Active TSS	Duodenum Smooth Muscle	Duodenum
20	chr9:72871000-72872000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr9:72871000-72872000	Flanking Active TSS	HSMMtube	muscle
22	chr9:72871000-72872600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr9:72871000-72872600	Active TSS	Fetal Brain Male	brain
24	chr9:72871000-72873200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr9:72871000-72876200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr9:72871200-72872200	Active TSS	NHLF	lung
27	chr9:72871200-72872600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr9:72871200-72873000	Enhancers	Brain Substantia Nigra	brain
29	chr9:72871200-72873200	Weak transcription	Small Intestine	intestine
30	chr9:72871400-72872200	Enhancers	Cortex derived primary cultured neurospheres	brain
31	chr9:72871400-72872200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr9:72871400-72872400	Weak transcription	Brain Angular Gyrus	brain
33	chr9:72871400-72872600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
34	chr9:72871400-72873000	Enhancers	Brain Hippocampus Middle	brain
35	chr9:72871400-72873000	Enhancers	NHDF-Ad	bronchial
36	chr9:72871400-72873200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr9:72871400-72873200	Active TSS	Colonic Mucosa	Colon
38	chr9:72871600-72872000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
39	chr9:72871600-72872000	Weak transcription	Brain Inferior Temporal Lobe	brain
40	chr9:72871600-72872000	Active TSS	Colon Smooth Muscle	Colon
41	chr9:72871600-72872000	Flanking Active TSS	Pancreas	Pancrea
42	chr9:72871600-72872000	Flanking Active TSS	HepG2	liver
43	chr9:72871600-72872200	Enhancers	Skeletal Muscle Female	skeletal muscle
44	chr9:72871600-72872400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr9:72871600-72872400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr9:72871600-72872400	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr9:72871600-72872400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr9:72871600-72872400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
49	chr9:72871600-72872400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr9:72871600-72872600	Enhancers	Fetal Intestine Large	intestine

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