Variant report

Variant	rs2272459
Chromosome Location	chr15:93527794-93527795
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10520717	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10520719	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11074126	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11074127	0.80[AMR][1000 genomes]
rs11630052	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11630582	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11631553	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632522	0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs11634204	0.85[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs11634207	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11637047	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637185	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11857145	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12594991	0.87[ASN][1000 genomes]
rs12904680	0.82[AMR][1000 genomes]
rs12906132	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12907579	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1534779	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17525800	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2033844	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2119010	0.80[AMR][1000 genomes]
rs2272457	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28540863	0.82[AMR][1000 genomes]
rs28668136	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34026217	0.83[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs35327372	0.82[AMR][1000 genomes]
rs35477598	0.88[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs35596808	0.87[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs36048863	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3784786	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3817597	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4778062	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4778065	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56358327	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs66726419	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948738	chr15:93070742-93728147	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	169 gene(s)	inside rSNPs	diseases
2	nsv1049490	chr15:93134405-93591660	Enhancers Genic enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	151 gene(s)	inside rSNPs	diseases
3	nsv530846	chr15:93323949-94030462	Active TSS Strong transcription Flanking Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	153 gene(s)	inside rSNPs	diseases
4	nsv948881	chr15:93383740-93603608	Genic enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	nsv530847	chr15:93444024-93555676	Strong transcription Weak transcription Enhancers Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
6	nsv917347	chr15:93444094-93586814	Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2272459	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93493200-93533000	Strong transcription	Cortex derived primary cultured neurospheres	brain
2	chr15:93493200-93536000	Strong transcription	HSMM	muscle
3	chr15:93493200-93571000	Strong transcription	Dnd41	blood
4	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
5	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
6	chr15:93493400-93568600	Strong transcription	Liver	Liver
7	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
8	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
10	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr15:93493800-93532600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
15	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
16	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
18	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
19	chr15:93494400-93540600	Strong transcription	Primary T cells from cord blood	blood
20	chr15:93504000-93567800	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr15:93505000-93569800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr15:93506000-93569800	Strong transcription	HepG2	liver
23	chr15:93506400-93561800	Strong transcription	A549	lung
24	chr15:93506400-93569600	Strong transcription	Fetal Muscle Trunk	muscle
25	chr15:93507000-93532800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr15:93508000-93532600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr15:93509600-93535400	Strong transcription	Fetal Muscle Leg	muscle
28	chr15:93509600-93542400	Strong transcription	Hela-S3	cervix
29	chr15:93509600-93568000	Strong transcription	Primary B cells from cord blood	blood
30	chr15:93509600-93569600	Strong transcription	NHDF-Ad	bronchial
31	chr15:93509600-93571200	Strong transcription	Fetal Lung	lung
32	chr15:93509600-93571400	Strong transcription	Duodenum Mucosa	Duodenum
33	chr15:93509800-93568600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:93509800-93572000	Strong transcription	Fetal Intestine Large	intestine
35	chr15:93512600-93529400	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
36	chr15:93512800-93537400	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
37	chr15:93512800-93541200	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr15:93512800-93560200	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr15:93512800-93568000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
42	chr15:93513400-93545400	Strong transcription	Adipose Nuclei	Adipose
43	chr15:93513800-93560000	Strong transcription	Fetal Kidney	kidney
44	chr15:93514200-93561000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr15:93514200-93570800	Strong transcription	H1 Cell Line	embryonic stem cell
46	chr15:93514400-93535400	Strong transcription	HSMMtube	muscle
47	chr15:93515000-93561000	Strong transcription	Monocytes-CD14+_RO01746	blood
48	chr15:93515200-93533600	Strong transcription	Fetal Stomach	stomach
49	chr15:93515400-93537000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
50	chr15:93515600-93533800	Strong transcription	Thymus	Thymus

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