Variant report

Variant	rs2388055
Chromosome Location	chr15:93539666-93539667
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93539666-93539758	K562	blood:	n/a	n/a

Variant related genes	Relation type
CHD2	TF binding region

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10520718	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1074512	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1074513	0.88[EUR][1000 genomes]
rs11074120	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634566	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes]
rs11857466	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11857669	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438635	0.91[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs12591124	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12592920	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12594474	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12594991	0.81[AMR][1000 genomes]
rs12909677	0.88[EUR][1000 genomes]
rs12914956	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17610487	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1881834	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2388054	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs34448107	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs36032658	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3736619	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3784785	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826035	0.83[AMR][1000 genomes]
rs59253118	0.87[EUR][1000 genomes]
rs62023146	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6497011	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6497013	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7174043	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7176652	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7179863	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8026679	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8042395	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8042632	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs9302362	0.85[AMR][1000 genomes];0.84[EUR][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
rs2388055	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	chr15:93493200-93571000	Strong transcription	Dnd41	blood
2	chr15:93493200-93571200	Strong transcription	Rectal Mucosa Donor 29	rectum
3	chr15:93493400-93548000	Strong transcription	Muscle Satellite Cultured Cells	--
4	chr15:93493400-93568600	Strong transcription	Liver	Liver
5	chr15:93493400-93569600	Strong transcription	Placenta	Placenta
6	chr15:93493400-93571000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr15:93493400-93571000	Strong transcription	Rectal Mucosa Donor 31	rectum
8	chr15:93493600-93571400	Strong transcription	HUES6 Cell Line	embryonic stem cell
9	chr15:93493800-93561400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:93493800-93571400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:93494000-93568200	Strong transcription	Fetal Thymus	thymus
12	chr15:93494000-93570400	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:93494000-93570800	Strong transcription	HUES64 Cell Line	embryonic stem cell
14	chr15:93494000-93571000	Strong transcription	HUES48 Cell Line	embryonic stem cell
15	chr15:93494000-93571400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:93494400-93540600	Strong transcription	Primary T cells from cord blood	blood
17	chr15:93504000-93567800	Strong transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:93505000-93569800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
19	chr15:93506000-93569800	Strong transcription	HepG2	liver
20	chr15:93506400-93561800	Strong transcription	A549	lung
21	chr15:93506400-93569600	Strong transcription	Fetal Muscle Trunk	muscle
22	chr15:93509600-93542400	Strong transcription	Hela-S3	cervix
23	chr15:93509600-93568000	Strong transcription	Primary B cells from cord blood	blood
24	chr15:93509600-93569600	Strong transcription	NHDF-Ad	bronchial
25	chr15:93509600-93571200	Strong transcription	Fetal Lung	lung
26	chr15:93509600-93571400	Strong transcription	Duodenum Mucosa	Duodenum
27	chr15:93509800-93568600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:93509800-93572000	Strong transcription	Fetal Intestine Large	intestine
29	chr15:93512800-93541200	Strong transcription	Primary T cells fromperipheralblood	blood
30	chr15:93512800-93560200	Strong transcription	Primary monocytes fromperipheralblood	blood
31	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:93512800-93567800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:93512800-93568000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:93513400-93545400	Strong transcription	Adipose Nuclei	Adipose
35	chr15:93513800-93560000	Strong transcription	Fetal Kidney	kidney
36	chr15:93514200-93561000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr15:93514200-93570800	Strong transcription	H1 Cell Line	embryonic stem cell
38	chr15:93515000-93561000	Strong transcription	Monocytes-CD14+_RO01746	blood
39	chr15:93519200-93548600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
40	chr15:93521200-93568200	Strong transcription	Primary hematopoietic stem cells	blood
41	chr15:93521600-93548000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr15:93521600-93568000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr15:93521800-93569400	Strong transcription	Duodenum Smooth Muscle	Duodenum
44	chr15:93522800-93547800	Strong transcription	Osteobl	bone
45	chr15:93522800-93563200	Strong transcription	GM12878-XiMat	blood
46	chr15:93523000-93570600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr15:93523200-93545400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
48	chr15:93524600-93548800	Strong transcription	Colon Smooth Muscle	Colon
49	chr15:93525600-93563600	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
50	chr15:93525600-93570600	Strong transcription	NH-A	brain

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