Variant report

Variant	rs920389
Chromosome Location	chr15:93421733-93421734
allele	C/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	UBTF	chr15:93421676-93422481	K562	blood:	n/a	n/a
2	GATA1	chr15:93420919-93422547	PBDE	blood:	n/a	chr15:93421878-93421895 chr15:93422371-93422382 chr15:93421942-93421952
3	REST	chr15:93421730-93422196	K562	blood:	n/a	chr15:93421841-93421850
4	GATA2	chr15:93421661-93422030	K562	blood:	n/a	chr15:93421878-93421895 chr15:93421942-93421952
5	CBX3	chr15:93421480-93422569	K562	blood:	n/a	n/a
6	RCOR1	chr15:93421614-93422193	K562	blood:	n/a	n/a
7	TBP	chr15:93421712-93422263	K562	blood:	n/a	n/a
8	USF1	chr15:93421695-93422315	K562	blood:	n/a	chr15:93422105-93422116
9	HMGN3	chr15:93421420-93422265	K562	blood:	n/a	n/a
10	HCFC1	chr15:93421611-93422130	K562	blood:	n/a	n/a
11	BHLHE40	chr15:93421618-93422257	K562	blood:	n/a	n/a
12	EP300	chr15:93421723-93422363	K562	blood:	n/a	n/a
13	POLR2A	chr15:93421680-93422240	K562	blood:	n/a	n/a
14	TBL1XR1	chr15:93421662-93422345	K562	blood:	n/a	n/a
15	MAZ	chr15:93421662-93422146	K562	blood:	n/a	chr15:93422104-93422117 chr15:93422106-93422115
16	TEAD4	chr15:93421510-93422389	K562	blood:	n/a	n/a
17	POLR2A	chr15:93421727-93422128	K562	blood:	n/a	n/a
18	CCNT2	chr15:93421554-93422298	K562	blood:	n/a	chr15:93421878-93421898
19	MYC	chr15:93421727-93422322	K562	blood:	n/a	chr15:93422104-93422117 chr15:93422106-93422115
20	ZC3H11A	chr15:93421496-93422351	K562	blood:	n/a	n/a
21	RCOR1	chr15:93421599-93422480	K562	blood:	n/a	n/a
22	TEAD4	chr15:93421605-93422277	K562	blood:	n/a	n/a
23	POLR2A	chr15:93421552-93422340	K562	blood:	n/a	n/a
24	JUN	chr15:93421608-93422363	K562	blood:	n/a	n/a
25	MAX	chr15:93421556-93422227	K562	blood:	n/a	chr15:93422104-93422117 chr15:93422106-93422115
26	EP300	chr15:93421668-93422458	K562	blood:	n/a	n/a
27	GATA1	chr15:93421708-93422165	PBDEFetal	blood:	n/a	chr15:93421878-93421895 chr15:93421942-93421952
28	SMC3	chr15:93421622-93421822	K562	blood:	n/a	n/a
29	NR2F2	chr15:93421710-93422127	K562	blood:	n/a	n/a
30	TBL1XR1	chr15:93421512-93422267	K562	blood:	n/a	n/a
31	TAL1	chr15:93421646-93422576	K562	blood:	n/a	chr15:93421878-93421896
32	NR2F2	chr15:93421606-93422575	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93392783..93395116-chr15:93420649..93423095,2	K562	blood:
2	chr15:93333327..93367027-chr15:93419774..93462750,363	K562	blood:
3	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
4	chr15:93413461..93416683-chr15:93420184..93421907,3	K562	blood:
5	chr15:93337836..93370220-chr15:93420085..93452591,332	K562	blood:
6	chr15:93345383..93371459-chr15:93416796..93454653,318	MCF-7	breast:
7	chr15:93314139..93315981-chr15:93421509..93423581,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000272888	TF binding region
CHD2	TF binding region
ENSG00000185442	Chromatin interaction
ENSG00000258527	Chromatin interaction
ENSG00000258922	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10520716	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs12437674	0.86[JPT][hapmap]
rs12443243	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs12901950	0.84[JPT][hapmap]
rs12904680	0.84[JPT][hapmap]
rs12916015	0.84[JPT][hapmap]
rs1318689	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs1320819	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1406714	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs1881835	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1978878	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3826036	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs4327000	0.86[JPT][hapmap]
rs4778052	1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];1.00[ASN][1000 genomes]
rs6497010	0.84[CHB][hapmap]
rs7164668	0.86[CHB][hapmap];0.86[JPT][hapmap]
rs7167194	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs7173103	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7176652	0.84[CHB][hapmap]
rs8024528	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs8026695	0.84[CHB][hapmap];0.92[JPT][hapmap]
rs8035739	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs961233	0.92[JPT][hapmap]

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	nsv904499	chr15:92914795-93472582	Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	163 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	nsv1047496	chr15:93412778-93475878	Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Weak transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1036560	chr15:93413594-93462163	Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs920389	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93412600-93425000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr15:93413600-93421800	Weak transcription	Gastric	stomach
3	chr15:93413600-93421800	Weak transcription	Skeletal Muscle Male	skeletal muscle
4	chr15:93413600-93425200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
6	chr15:93414000-93424200	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:93418200-93423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr15:93419800-93424200	Enhancers	HepG2	liver
9	chr15:93420000-93422200	Enhancers	Fetal Muscle Leg	muscle
10	chr15:93420000-93425200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
11	chr15:93420200-93421800	Enhancers	Ovary	ovary
12	chr15:93420200-93422600	Enhancers	Fetal Intestine Large	intestine
13	chr15:93420200-93423200	Enhancers	Thymus	Thymus
14	chr15:93420200-93423600	Enhancers	Fetal Thymus	thymus
15	chr15:93420200-93425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:93420200-93425000	Enhancers	Fetal Heart	heart
17	chr15:93420400-93423200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:93420400-93423200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr15:93420400-93424000	Weak transcription	Hela-S3	cervix
20	chr15:93420400-93425200	Weak transcription	Psoas Muscle	Psoas
21	chr15:93420600-93421800	Weak transcription	Dnd41	blood
22	chr15:93420600-93423600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
23	chr15:93420600-93424200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr15:93420600-93424600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
25	chr15:93420800-93421800	Enhancers	Primary B cells from peripheral blood	blood
26	chr15:93420800-93422600	Enhancers	A549	lung
27	chr15:93420800-93423400	Enhancers	Primary T cells from cord blood	blood
28	chr15:93420800-93423800	Weak transcription	Fetal Stomach	stomach
29	chr15:93420800-93424200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr15:93421000-93421800	Weak transcription	Placenta	Placenta
31	chr15:93421000-93423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
32	chr15:93421000-93424000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:93421000-93424800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr15:93421200-93422200	Enhancers	Spleen	Spleen
35	chr15:93421200-93422600	Enhancers	Fetal Intestine Small	intestine
36	chr15:93421400-93424200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr15:93421400-93424200	Enhancers	Primary T helper cells PMA-I stimulated	--
38	chr15:93421400-93424400	Enhancers	Primary T cells fromperipheralblood	blood
39	chr15:93421400-93424600	Enhancers	Primary T helper cells fromperipheralblood	blood
40	chr15:93421400-93425200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:93421600-93421800	Enhancers	Right Atrium	heart
42	chr15:93421600-93422000	Enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr15:93421600-93422200	Enhancers	H1 Cell Line	embryonic stem cell
44	chr15:93421600-93422200	Enhancers	HUES6 Cell Line	embryonic stem cell
45	chr15:93421600-93422200	Enhancers	iPS-15b Cell Line	embryonic stem cell
46	chr15:93421600-93422200	Enhancers	Duodenum Mucosa	Duodenum
47	chr15:93421600-93422200	Enhancers	Pancreas	Pancrea
48	chr15:93421600-93422200	Enhancers	Skeletal Muscle Female	skeletal muscle
49	chr15:93421600-93422200	Enhancers	Stomach Smooth Muscle	stomach
50	chr15:93421600-93422400	Enhancers	Fetal Kidney	kidney

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