Variant report

Variant	rs4778052
Chromosome Location	chr15:93421244-93421245
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	GATA1	chr15:93420919-93422547	PBDE	blood:	n/a	chr15:93421878-93421895 chr15:93422371-93422382 chr15:93421942-93421952
2	ZNF384	chr15:93420351-93421463	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:

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

Extended variants
information (count: 30 )
Associated
traits (count: 2 )

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	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1320819	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs1406714	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs1881835	0.92[CHB][hapmap];0.85[JPT][hapmap]
rs1978878	1.00[ASN][1000 genomes]
rs3826036	0.92[CHB][hapmap];0.86[JPT][hapmap]
rs4327000	0.86[JPT][hapmap]
rs6497010	0.83[CHB][hapmap]
rs7164668	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7167194	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs7173103	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs7176652	0.83[CHB][hapmap]
rs8024528	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs8026695	0.83[CHB][hapmap];0.92[JPT][hapmap]
rs8035739	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs920389	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]
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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4778052	CHD2	Cis_1M	lymphoblastoid	RTeQTL
rs4778052	RHCG	cis	parietal	SCAN

Chromatin state (count:42 , 50 per page) page: 1

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	chr15:93413800-93421600	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr15:93413800-93421600	Weak transcription	Pancreas	Pancrea
7	chr15:93413800-93421600	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:93413800-93425200	Weak transcription	Left Ventricle	heart
9	chr15:93414000-93424200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:93418200-93423200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr15:93419400-93421600	Enhancers	K562	blood
12	chr15:93419800-93424200	Enhancers	HepG2	liver
13	chr15:93420000-93422200	Enhancers	Fetal Muscle Leg	muscle
14	chr15:93420000-93425200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
15	chr15:93420200-93421800	Enhancers	Ovary	ovary
16	chr15:93420200-93422600	Enhancers	Fetal Intestine Large	intestine
17	chr15:93420200-93423200	Enhancers	Thymus	Thymus
18	chr15:93420200-93423600	Enhancers	Fetal Thymus	thymus
19	chr15:93420200-93425000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr15:93420200-93425000	Enhancers	Fetal Heart	heart
21	chr15:93420400-93423200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:93420400-93423200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:93420400-93424000	Weak transcription	Hela-S3	cervix
24	chr15:93420400-93425200	Weak transcription	Psoas Muscle	Psoas
25	chr15:93420600-93421800	Weak transcription	Dnd41	blood
26	chr15:93420600-93423600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr15:93420600-93424200	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr15:93420600-93424600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:93420800-93421800	Enhancers	Primary B cells from peripheral blood	blood
30	chr15:93420800-93422600	Enhancers	A549	lung
31	chr15:93420800-93423400	Enhancers	Primary T cells from cord blood	blood
32	chr15:93420800-93423800	Weak transcription	Fetal Stomach	stomach
33	chr15:93420800-93424200	Enhancers	Primary T killer memory cells from peripheral blood	blood
34	chr15:93421000-93421400	Weak transcription	Primary T cells fromperipheralblood	blood
35	chr15:93421000-93421400	Weak transcription	Primary T helper cells PMA-I stimulated	--
36	chr15:93421000-93421400	Weak transcription	Primary T helper cells fromperipheralblood	blood
37	chr15:93421000-93421800	Weak transcription	Placenta	Placenta
38	chr15:93421000-93423200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr15:93421000-93424000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:93421000-93424800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
41	chr15:93421200-93422200	Enhancers	Spleen	Spleen
42	chr15:93421200-93422600	Enhancers	Fetal Intestine Small	intestine

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