Variant report

Variant	rs4327000
Chromosome Location	chr15:93492811-93492812
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:22)
CpG islands
(count:0)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:22 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	KAP1	chr15:93492281-93493708	K562	blood:	n/a	n/a
2	CBX3	chr15:93492606-93493410	K562	blood:	n/a	n/a
3	EP300	chr15:93492788-93492812	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:93492671-93493341	K562	blood:	n/a	n/a
5	RCOR1	chr15:93492737-93493356	IMR90	lung:	n/a	n/a
6	CBX3	chr15:93492653-93493221	K562	blood:	n/a	n/a
7	SETDB1	chr15:93491927-93494250	K562	blood:	n/a	n/a
8	KAP1	chr15:93492620-93493565	HEK293	kidney:	n/a	n/a
9	POLR2A	chr15:93492619-93493386	A549	lung:	n/a	n/a
10	POLR2A	chr15:93492704-93492853	H1-hESC	embryonic stem cell:	n/a	n/a
11	ARID3A	chr15:93492692-93492824	HepG2	liver:	n/a	n/a
12	SETDB1	chr15:93492483-93493794	U2OS	brain:	n/a	n/a
13	POLR2A	chr15:93492522-93494227	HepG2	liver:	n/a	n/a
14	TCF12	chr15:93492637-93493382	A549	lung:	n/a	n/a
15	USF1	chr15:93492783-93493237	HCT-116	colon:	n/a	n/a
16	POLR2A	chr15:93492624-93493439	H1-hESC	embryonic stem cell:	n/a	n/a
17	POLR2A	chr15:93492791-93493491	GM12891	blood:	n/a	n/a
18	GATA3	chr15:93492750-93492923	SH-SY5Y	brain:	n/a	n/a
19	TRIM28	chr15:93492692-93493307	K562	blood:	n/a	n/a
20	KAP1	chr15:93492612-93493630	U2OS	brain:	n/a	n/a
21	POLR2A	chr15:93492070-93502707	K562	blood:	n/a	n/a
22	CBX3	chr15:93492735-93493393	HCT-116	colon:	n/a	n/a

No data

Variant related genes	Relation type
CHD2	TF binding region

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

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

rs_ID	r²[population]
rs10520716	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11634566	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.91[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12438635	0.88[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.89[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12594991	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs12901950	0.86[JPT][hapmap]
rs12904680	0.86[JPT][hapmap]
rs12905312	0.83[EUR][1000 genomes]
rs12908494	0.87[EUR][1000 genomes]
rs12916015	0.86[JPT][hapmap]
rs1318689	0.93[JPT][hapmap]
rs1320819	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1406714	0.93[JPT][hapmap]
rs1881835	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[JPT][hapmap];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35865218	0.90[ASN][1000 genomes]
rs3743469	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826035	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs3826036	1.00[CEU][hapmap];0.85[CHB][hapmap];0.85[JPT][hapmap];0.86[EUR][1000 genomes]
rs4778052	0.86[JPT][hapmap]
rs6497009	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6497010	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7164668	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7168780	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7171151	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7173103	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175134	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7176652	0.93[CHB][hapmap]
rs8024528	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs8026695	0.93[JPT][hapmap]
rs8035739	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs920389	0.86[JPT][hapmap]
rs9302362	0.81[JPT][hapmap]
rs961233	0.93[JPT][hapmap]

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
rs4327000	CHD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
2	chr15:93477200-93493000	Strong transcription	Placenta	Placenta
3	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr15:93478600-93503200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr15:93480400-93493000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr15:93480800-93494000	Strong transcription	Skeletal Muscle Male	skeletal muscle
7	chr15:93485000-93494600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
8	chr15:93486000-93495000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:93486400-93493800	Strong transcription	Fetal Brain Male	brain
10	chr15:93486800-93493200	ZNF genes & repeats	Dnd41	blood
11	chr15:93486800-93494400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
12	chr15:93487600-93494000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:93487600-93500000	Strong transcription	Brain Angular Gyrus	brain
14	chr15:93488200-93493000	Strong transcription	Lung	lung
15	chr15:93488200-93493200	Strong transcription	Pancreas	Pancrea
16	chr15:93488200-93493600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
17	chr15:93488200-93494000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr15:93488200-93494000	ZNF genes & repeats	Thymus	Thymus
19	chr15:93488200-93494000	ZNF genes & repeats	GM12878-XiMat	blood
20	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr15:93488400-93493800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
23	chr15:93489000-93494000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
24	chr15:93489200-93493400	ZNF genes & repeats	Primary B cells from cord blood	blood
25	chr15:93489200-93493800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr15:93489200-93493800	Strong transcription	Placenta Amnion	Placenta Amnion
27	chr15:93489200-93494000	Strong transcription	Ovary	ovary
28	chr15:93489400-93493000	ZNF genes & repeats	K562	blood
29	chr15:93489400-93494000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
30	chr15:93489400-93494000	ZNF genes & repeats	NHEK	skin
31	chr15:93489400-93494200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
32	chr15:93489400-93494400	ZNF genes & repeats	Primary T cells from cord blood	blood
33	chr15:93489600-93494000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
34	chr15:93489800-93494000	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:93489800-93494000	ZNF genes & repeats	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr15:93489800-93494000	ZNF genes & repeats	Fetal Intestine Small	intestine
37	chr15:93489800-93494000	ZNF genes & repeats	Fetal Thymus	thymus
38	chr15:93489800-93494800	Strong transcription	Gastric	stomach
39	chr15:93490000-93493200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
40	chr15:93490000-93493400	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
41	chr15:93490000-93493400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
42	chr15:93490000-93493600	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
43	chr15:93490000-93493600	ZNF genes & repeats	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:93490200-93493400	ZNF genes & repeats	Liver	Liver
45	chr15:93490200-93493800	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:93490200-93493800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
47	chr15:93490200-93494000	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
48	chr15:93490200-93494000	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
49	chr15:93490200-93494000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr15:93490200-93494000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood

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