Variant report

Variant	rs10123651
Chromosome Location	chr9:15439860-15439861
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 69 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10117375	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117803	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10117823	1.00[CEU][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10121012	0.83[AMR][1000 genomes]
rs10125713	0.86[YRI][hapmap];0.92[AMR][1000 genomes]
rs10962054	0.85[AMR][1000 genomes]
rs12337310	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs12344963	0.92[AMR][1000 genomes]
rs12350062	0.92[AMR][1000 genomes]
rs12350903	0.83[AMR][1000 genomes]
rs12859	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs175762	0.85[AMR][1000 genomes]
rs2064030	0.92[YRI][hapmap];0.87[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2488959	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490849	0.94[ASN][1000 genomes]
rs2490850	0.89[ASN][1000 genomes]
rs2490851	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490852	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490853	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490854	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490855	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490856	1.00[ASN][1000 genomes]
rs2490857	1.00[ASN][1000 genomes]
rs2490858	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2490859	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2665515	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2737840	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs276445	0.83[AMR][1000 genomes]
rs276446	0.83[AMR][1000 genomes]
rs276450	0.83[AMR][1000 genomes]
rs276451	0.83[AMR][1000 genomes]
rs2777951	0.92[AMR][1000 genomes]
rs2795125	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes]
rs2795128	0.92[YRI][hapmap];0.85[AMR][1000 genomes]
rs2798701	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798702	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798703	1.00[ASN][1000 genomes]
rs2798704	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798705	0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2798717	1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804992	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804993	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2804994	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2821525	0.92[AMR][1000 genomes]
rs2821529	0.85[AMR][1000 genomes]
rs2821530	0.93[YRI][hapmap];0.92[AMR][1000 genomes]
rs2821543	0.83[AMR][1000 genomes]
rs2821544	0.83[AMR][1000 genomes]
rs28497163	0.85[AMR][1000 genomes]
rs28796681	0.83[AMR][1000 genomes]
rs28800775	0.83[AMR][1000 genomes]
rs3119700	0.83[AMR][1000 genomes]
rs3122705	0.83[AMR][1000 genomes]
rs3129711	0.83[AMR][1000 genomes]
rs365710	0.83[AMR][1000 genomes]
rs413356	0.83[AMR][1000 genomes]
rs418153	0.83[AMR][1000 genomes]
rs741930	0.92[YRI][hapmap];0.92[AMR][1000 genomes]
rs7852936	0.92[AMR][1000 genomes]
rs796391	0.83[AMR][1000 genomes]
rs926154	0.86[YRI][hapmap];0.92[AMR][1000 genomes]
rs9298729	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv517975	chr9:15286446-15534070	Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv892625	chr9:15326251-16064850	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv1030287	chr9:15332709-15458001	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv892626	chr9:15389610-15694690	Flanking Active TSS Active TSS Weak transcription Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv892627	chr9:15397969-15909450	Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
6	nsv831520	chr9:15404866-15444447	Weak transcription Active TSS Strong transcription Genic enhancers Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases
7	nsv892628	chr9:15420805-15528290	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS 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	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:15424000-15443400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr9:15424000-15443600	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr9:15426200-15441800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr9:15426400-15441800	Weak transcription	Spleen	Spleen
5	chr9:15426400-15442800	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr9:15426400-15443600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr9:15426400-15443600	Weak transcription	Gastric	stomach
8	chr9:15426400-15468200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr9:15426600-15442400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr9:15426600-15443400	Weak transcription	Fetal Heart	heart
11	chr9:15427000-15443400	Weak transcription	NHEK	skin
12	chr9:15431400-15441800	Weak transcription	Lung	lung
13	chr9:15431400-15442400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr9:15431400-15442800	Weak transcription	Brain Angular Gyrus	brain
15	chr9:15431400-15443400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr9:15431400-15443400	Weak transcription	Pancreas	Pancrea
17	chr9:15431400-15443600	Weak transcription	Aorta	Aorta
18	chr9:15431400-15443600	Weak transcription	Brain Cingulate Gyrus	brain
19	chr9:15431400-15443600	Weak transcription	Esophagus	oesophagus
20	chr9:15431400-15445800	Weak transcription	Right Ventricle	heart
21	chr9:15431400-15446000	Weak transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:15431400-15447800	Weak transcription	Psoas Muscle	Psoas
23	chr9:15431600-15443400	Weak transcription	Stomach Mucosa	stomach
24	chr9:15432200-15443600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
25	chr9:15433000-15440600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:15433000-15440600	Strong transcription	Fetal Intestine Large	intestine
27	chr9:15433400-15492400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr9:15433600-15440600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr9:15433600-15440600	Strong transcription	Fetal Thymus	thymus
30	chr9:15433600-15441000	Strong transcription	Rectal Mucosa Donor 31	rectum
31	chr9:15433600-15441200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
32	chr9:15433600-15441200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr9:15433600-15442000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:15433800-15440400	Strong transcription	Primary hematopoietic stem cells	blood
35	chr9:15433800-15441200	Strong transcription	Fetal Lung	lung
36	chr9:15434000-15464000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr9:15434400-15443400	Weak transcription	Colon Smooth Muscle	Colon
38	chr9:15434400-15443600	Weak transcription	Brain Hippocampus Middle	brain
39	chr9:15434400-15443600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
40	chr9:15434400-15443600	Weak transcription	K562	blood
41	chr9:15434400-15443800	Weak transcription	HSMMtube	muscle
42	chr9:15434600-15441200	Strong transcription	Primary monocytes fromperipheralblood	blood
43	chr9:15434600-15441800	Weak transcription	Thymus	Thymus
44	chr9:15434800-15441200	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr9:15434800-15442600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr9:15434800-15443600	Weak transcription	Rectal Smooth Muscle	rectum
47	chr9:15434800-15443600	Weak transcription	Stomach Smooth Muscle	stomach
48	chr9:15435000-15443200	Weak transcription	Brain Anterior Caudate	brain
49	chr9:15435000-15443400	Weak transcription	Fetal Brain Male	brain
50	chr9:15435000-15443400	Weak transcription	Ovary	ovary

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