Variant report

Variant	rs9920042
Chromosome Location	chr15:58901396-58901397
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:58888535..58891486-chr15:58900584..58902210,3	K562	blood:

Extended variants
information (count: 100 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs10851639	0.84[ASN][1000 genomes]
rs11071391	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11071392	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11071393	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12437457	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12437955	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs12438487	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438810	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12439189	0.83[ASN][1000 genomes]
rs12440091	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12440246	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12442451	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12442956	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12591291	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12591543	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12592332	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592750	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12708455	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12901989	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12905110	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs12905173	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12906705	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12906714	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12907237	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12908449	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12912286	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12915950	0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12916010	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12917500	0.85[EUR][1000 genomes]
rs12917577	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1365772	0.84[ASN][1000 genomes]
rs16940587	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940589	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940647	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16940651	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17301905	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1820548	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1869135	0.82[ASN][1000 genomes]
rs2081703	0.83[ASN][1000 genomes]
rs2303532	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2305421	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28417700	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28455654	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28457680	1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28542491	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28549001	0.81[AMR][1000 genomes]
rs28573205	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28576281	0.80[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs28584993	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28600144	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28609304	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28637832	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28639679	0.83[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28678478	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28722857	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28724298	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28728383	0.80[AMR][1000 genomes]
rs28734088	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs28852159	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34793995	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35499736	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3764196	0.82[ASN][1000 genomes]
rs4775084	0.84[ASN][1000 genomes]
rs6494030	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6494031	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6494032	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494033	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6494034	0.81[AMR][1000 genomes]
rs6494038	0.83[AMR][1000 genomes]
rs7163733	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7163939	0.81[AMR][1000 genomes]
rs7164620	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165035	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7165259	0.83[ASN][1000 genomes]
rs7165402	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7166076	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7166325	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7167528	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7170314	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7174175	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174386	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7174414	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7178954	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7180550	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8026668	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8033565	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8035960	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8036005	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8036448	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes]
rs8039791	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8040358	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9302203	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9635351	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9744518	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920310	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9920720	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9921024	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats 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	50 gene(s)	inside rSNPs	diseases
3	nsv1551	chr15:58891639-58936580	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:117 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58878800-58904400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:58880200-58904600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:58880600-58920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:58882600-58904000	Weak transcription	Gastric	stomach
5	chr15:58882600-58907600	Weak transcription	Placenta Amnion	Placenta Amnion
6	chr15:58883000-58901800	Weak transcription	HUVEC	blood vessel
7	chr15:58883200-58904600	Strong transcription	HSMM	muscle
8	chr15:58884400-58902600	Weak transcription	Cortex derived primary cultured neurospheres	brain
9	chr15:58885800-58906800	Weak transcription	Fetal Brain Male	brain
10	chr15:58887200-58906600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
11	chr15:58887800-58905200	Weak transcription	Brain Germinal Matrix	brain
12	chr15:58888000-58906200	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr15:58888400-58920000	Weak transcription	Rectal Smooth Muscle	rectum
14	chr15:58889600-58902000	Weak transcription	HMEC	breast
15	chr15:58889600-58904600	Weak transcription	Colonic Mucosa	Colon
16	chr15:58889600-58905200	Weak transcription	Fetal Brain Female	brain
17	chr15:58889600-58919800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:58889800-58901400	Weak transcription	Duodenum Mucosa	Duodenum
19	chr15:58889800-58918800	Weak transcription	Osteobl	bone
20	chr15:58889800-58921000	Weak transcription	Ovary	ovary
21	chr15:58890000-58901400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr15:58890000-58904400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:58890000-58906200	Weak transcription	Small Intestine	intestine
24	chr15:58890800-58905200	Weak transcription	Brain Anterior Caudate	brain
25	chr15:58891000-58906800	Strong transcription	Monocytes-CD14+_RO01746	blood
26	chr15:58891400-58959600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:58892000-58902200	Weak transcription	A549	lung
28	chr15:58893200-58902600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr15:58893800-58901800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:58893800-58906200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:58893800-58906200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:58894400-58905200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr15:58894800-58904400	Weak transcription	Fetal Stomach	stomach
34	chr15:58894800-58904400	Weak transcription	Spleen	Spleen
35	chr15:58894800-58904600	Weak transcription	Aorta	Aorta
36	chr15:58894800-58906200	Strong transcription	Primary B cells from cord blood	blood
37	chr15:58894800-58906800	Weak transcription	Psoas Muscle	Psoas
38	chr15:58895800-58902600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:58896000-58902600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
40	chr15:58896600-58905000	Weak transcription	Lung	lung
41	chr15:58897200-58904000	Weak transcription	Rectal Mucosa Donor 31	rectum
42	chr15:58897200-58904600	Weak transcription	Pancreas	Pancrea
43	chr15:58897400-58901600	Weak transcription	Adipose Nuclei	Adipose
44	chr15:58897400-58901600	Weak transcription	Brain Hippocampus Middle	brain
45	chr15:58897400-58904200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
46	chr15:58897400-58905200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:58897600-58901400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr15:58897600-58901600	Weak transcription	HepG2	liver
49	chr15:58897600-58905000	Weak transcription	Stomach Smooth Muscle	stomach
50	chr15:58897800-58901400	Weak transcription	GM12878-XiMat	blood

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