Variant report

Variant	rs72618136
Chromosome Location	chr9:86299402-86299403
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr9:86298986..86303456-chr9:86320609..86324425,4	MCF-7	breast:
2	chr9:86294745..86296646-chr9:86298711..86300362,2	K562	blood:
3	chr18:40222756..40225050-chr9:86298792..86300940,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000135018	Chromatin interaction
ENSG00000254473	Chromatin interaction

Extended variants
information (count: 58 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10512136	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs10512137	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1056073	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10746717	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780616	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780617	0.88[AMR][1000 genomes]
rs10780618	0.86[AMR][1000 genomes]
rs10780619	0.87[AMR][1000 genomes]
rs10780620	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs10780622	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10780623	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10780624	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10780625	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10868035	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10868036	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10868037	0.86[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10868038	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10868042	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10868043	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11140198	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11140202	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140209	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11140212	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11140221	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11140223	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11791175	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12235741	0.83[AMR][1000 genomes]
rs1333861	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1333862	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1537502	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1537503	0.85[AMR][1000 genomes]
rs17080575	0.83[AMR][1000 genomes]
rs1961941	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2282220	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2811921	0.81[ASN][1000 genomes]
rs3750409	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs3750410	0.87[AMR][1000 genomes]
rs3814505	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3814507	0.83[AMR][1000 genomes]
rs4146740	0.82[EUR][1000 genomes]
rs4454364	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4877790	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4877791	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877793	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877794	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4877796	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4877797	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4877799	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4877800	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7046388	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7860614	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7863266	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs7866234	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7871055	0.86[AMR][1000 genomes]
rs868917	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[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	nsv893512	chr9:86022215-86323309	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1044639	chr9:86252505-86412041	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
3	nsv893513	chr9:86298632-86433459	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs72618136	RP11-522I20.3	cis	Muscle Skeletal	GTEx
rs72618136	RP11-522I20.3	cis	Whole Blood	GTEx

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:86260600-86300400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
2	chr9:86264800-86300200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
3	chr9:86273800-86304000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr9:86280400-86307400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr9:86282000-86300000	Strong transcription	Primary monocytes fromperipheralblood	blood
6	chr9:86289000-86304200	Weak transcription	Ovary	ovary
7	chr9:86289000-86308200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr9:86289000-86321800	Weak transcription	Esophagus	oesophagus
9	chr9:86291400-86314400	Weak transcription	Fetal Heart	heart
10	chr9:86291600-86300600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr9:86292800-86308600	Weak transcription	Brain Cingulate Gyrus	brain
12	chr9:86293600-86301200	Weak transcription	Aorta	Aorta
13	chr9:86293600-86301400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr9:86293600-86304200	Weak transcription	Brain Hippocampus Middle	brain
15	chr9:86293600-86317000	Weak transcription	NHLF	lung
16	chr9:86294000-86321800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
17	chr9:86294200-86305800	Weak transcription	Spleen	Spleen
18	chr9:86294200-86314200	Weak transcription	Gastric	stomach
19	chr9:86294200-86315600	Weak transcription	Right Ventricle	heart
20	chr9:86294200-86320000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr9:86295000-86301400	Weak transcription	Fetal Kidney	kidney
22	chr9:86295000-86308800	Weak transcription	Rectal Smooth Muscle	rectum
23	chr9:86295000-86313600	Weak transcription	Lung	lung
24	chr9:86296000-86300200	Weak transcription	Cortex derived primary cultured neurospheres	brain
25	chr9:86296000-86304000	Weak transcription	NHDF-Ad	bronchial
26	chr9:86296000-86320800	Weak transcription	Fetal Brain Female	brain
27	chr9:86296200-86316800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr9:86296400-86303000	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr9:86296400-86304200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
30	chr9:86296600-86303800	Weak transcription	Brain Substantia Nigra	brain
31	chr9:86296800-86299800	Weak transcription	A549	lung
32	chr9:86296800-86299800	Weak transcription	Hela-S3	cervix
33	chr9:86296800-86301400	Weak transcription	Skeletal Muscle Male	skeletal muscle
34	chr9:86296800-86302200	Weak transcription	Stomach Smooth Muscle	stomach
35	chr9:86296800-86303200	Weak transcription	Brain Germinal Matrix	brain
36	chr9:86296800-86306400	Weak transcription	Colon Smooth Muscle	Colon
37	chr9:86296800-86314200	Weak transcription	Primary hematopoietic stem cells	blood
38	chr9:86297000-86299600	Weak transcription	HSMMtube	muscle
39	chr9:86297000-86299800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr9:86297000-86301200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr9:86297000-86301400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr9:86297000-86304000	Weak transcription	Brain Angular Gyrus	brain
43	chr9:86297000-86304000	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr9:86297000-86315600	Weak transcription	HMEC	breast
45	chr9:86297000-86315600	Weak transcription	HSMM	muscle
46	chr9:86297000-86320000	Weak transcription	Rectal Mucosa Donor 29	rectum
47	chr9:86297200-86305400	Weak transcription	Psoas Muscle	Psoas
48	chr9:86297400-86301600	Weak transcription	Primary T cells from cord blood	blood
49	chr9:86297600-86299800	Weak transcription	NHEK	skin
50	chr9:86297600-86302600	Weak transcription	Duodenum Smooth Muscle	Duodenum

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