Variant report

Variant	rs58402825
Chromosome Location	chr9:116031366-116031367
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:116024711..116027399-chr9:116031082..116034074,3	MCF-7	breast:
2	chr9:116027249..116028822-chr9:116029570..116032042,2	MCF-7	breast:
3	chr9:115911868..115913830-chr9:116031326..116033544,3	K562	blood:
4	chr9:116031284..116035003-chr9:116035037..116039754,9	K562	blood:

Variant related genes	Relation type
ENSG00000136867	Chromatin interaction
ENSG00000136875	Chromatin interaction
ENSG00000176386	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10759634	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817463	0.83[ASN][1000 genomes]
rs10817464	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817466	0.83[ASN][1000 genomes]
rs10817469	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817471	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10817472	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981690	0.80[EUR][1000 genomes]
rs10981695	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10981705	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12336832	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12341669	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342197	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12342549	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12343330	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12348629	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349495	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12349500	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12349614	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12351168	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12351630	0.87[ASN][1000 genomes]
rs12352784	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12352925	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs17831256	1.00[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28733164	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs66509679	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72758255	0.84[EUR][1000 genomes]
rs7858741	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7863910	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530949	chr9:115821128-116487796	Flanking Active TSS Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
2	nsv1042663	chr9:115920158-116167140	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
3	nsv893744	chr9:115934852-116170227	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:115996000-116031600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
2	chr9:116008200-116037000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr9:116010200-116031800	Weak transcription	Fetal Heart	heart
4	chr9:116017600-116031800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr9:116018600-116036000	Strong transcription	Monocytes-CD14+_RO01746	blood
6	chr9:116019600-116033200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr9:116020600-116031600	Weak transcription	HUVEC	blood vessel
8	chr9:116021000-116036000	Strong transcription	Fetal Stomach	stomach
9	chr9:116021200-116031600	Weak transcription	Fetal Brain Male	brain
10	chr9:116021200-116032200	Weak transcription	Small Intestine	intestine
11	chr9:116021200-116032600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr9:116021400-116032200	Weak transcription	Pancreas	Pancrea
13	chr9:116022400-116036600	Weak transcription	Stomach Mucosa	stomach
14	chr9:116022600-116031600	Weak transcription	NHDF-Ad	bronchial
15	chr9:116022800-116031600	Weak transcription	Psoas Muscle	Psoas
16	chr9:116022800-116031800	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:116022800-116032200	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr9:116022800-116032200	Weak transcription	Esophagus	oesophagus
19	chr9:116022800-116036600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr9:116023000-116031400	Weak transcription	Muscle Satellite Cultured Cells	--
21	chr9:116023000-116031800	Weak transcription	NHLF	lung
22	chr9:116023000-116032200	Weak transcription	Gastric	stomach
23	chr9:116023000-116033000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr9:116023000-116033200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr9:116023000-116036800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr9:116023200-116031600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
27	chr9:116023200-116031800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
28	chr9:116023200-116031800	Weak transcription	Colon Smooth Muscle	Colon
29	chr9:116023400-116032200	Weak transcription	Right Ventricle	heart
30	chr9:116023400-116034200	Weak transcription	Colonic Mucosa	Colon
31	chr9:116023600-116032200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
32	chr9:116024600-116031600	Weak transcription	Hela-S3	cervix
33	chr9:116024800-116031800	Weak transcription	HSMMtube	muscle
34	chr9:116024800-116032200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:116024800-116032200	Weak transcription	Lung	lung
36	chr9:116025200-116031800	Weak transcription	HMEC	breast
37	chr9:116025400-116031400	Weak transcription	Brain Angular Gyrus	brain
38	chr9:116025400-116031400	Weak transcription	Fetal Brain Female	brain
39	chr9:116026000-116031600	Weak transcription	Brain Hippocampus Middle	brain
40	chr9:116026600-116035800	Strong transcription	Duodenum Smooth Muscle	Duodenum
41	chr9:116026800-116036000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr9:116027000-116035800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr9:116027000-116035800	Strong transcription	Skeletal Muscle Female	skeletal muscle
44	chr9:116027200-116031400	Strong transcription	Liver	Liver
45	chr9:116027200-116032200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr9:116027200-116033600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr9:116027200-116035200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
48	chr9:116027200-116035800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
49	chr9:116027200-116036000	Strong transcription	Primary monocytes fromperipheralblood	blood
50	chr9:116027200-116036000	Strong transcription	Rectal Mucosa Donor 29	rectum

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