Variant report

Variant	rs28573213
Chromosome Location	chr15:93464509-93464510
allele	A/G
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	chr15:93463603-93465528	K562	blood:	n/a	n/a
2	FOS	chr15:93463882-93465510	MCF10A-Er-Src	breast:	n/a	chr15:93465191-93465198 chr15:93465191-93465199 chr15:93465190-93465200 chr15:93465185-93465194 chr15:93465190-93465200 chr15:93465281-93465289 chr15:93465191-93465199
3	POLR2A	chr15:93463583-93466834	K562	blood:	n/a	n/a
4	FOS	chr15:93464073-93465478	MCF10A-Er-Src	breast:	n/a	chr15:93465191-93465198 chr15:93465191-93465199 chr15:93465190-93465200 chr15:93465185-93465194 chr15:93465190-93465200 chr15:93465281-93465289 chr15:93465191-93465199
5	POLR2A	chr15:93464339-93465399	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr15:93464004-93465380	GM12892	blood:	n/a	n/a
7	SP1	chr15:93464473-93465656	HCT-116	colon:	n/a	n/a
8	POLR2A	chr15:93463929-93464913	U87	brain:	n/a	n/a
9	POLR2A	chr15:93463691-93465348	PANC-1	pancreas:	n/a	n/a
10	POLR2A	chr15:93463784-93465404	PANC-1	pancreas:	n/a	n/a
11	GATA3	chr15:93464377-93464808	T-47D	breast:	n/a	chr15:93464606-93464615
12	POLR2A	chr15:93463568-93466760	U87	brain:	n/a	n/a
13	POLR2A	chr15:93463008-93472730	K562	blood:	n/a	n/a
14	WRNIP1	chr15:93464064-93465331	GM12878	blood:	n/a	n/a
15	POLR2A	chr15:93463976-93464552	U87	brain:	n/a	n/a
16	POLR2A	chr15:93464107-93465337	GM12891	blood:	n/a	n/a
17	SIN3AK20	chr15:93464464-93465536	HCT-116	colon:	n/a	n/a
18	POLR2A	chr15:93463684-93466928	GM12891	blood:	n/a	n/a
19	POLR2A	chr15:93464369-93464520	K562	blood:	n/a	n/a
20	POLR2A	chr15:93463762-93464552	U87	brain:	n/a	n/a
21	POLR2A	chr15:93463573-93465288	GM12878	blood:	n/a	n/a
22	POLR2A	chr15:93464040-93466615	GM12878	blood:	n/a	n/a
23	POLR2A	chr15:93462946-93466287	A549	lung:	n/a	n/a
24	CEBPB	chr15:93464480-93465460	Hela-S3	cervix:	n/a	n/a
25	POLR2A	chr15:93464030-93466292	GM12878	blood:	n/a	n/a
26	POLR2A	chr15:93462854-93466503	HepG2	liver:	n/a	n/a
27	CEBPB	chr15:93464418-93465709	HCT-116	colon:	n/a	n/a
28	POLR2A	chr15:93464340-93464728	K562	blood:	n/a	n/a
29	POLR2A	chr15:93464166-93464750	SK-N-MC	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93344712..93371031-chr15:93418700..93467618,365	MCF-7	breast:
2	chr15:93347226..93350141-chr15:93462968..93465327,2	MCF-7	breast:
3	chr15:93360172..93364704-chr15:93459982..93465049,6	MCF-7	breast:
4	chr15:93345806..93348640-chr15:93462884..93464595,2	K562	blood:
5	chr15:93463262..93465230-chr15:93468771..93470893,2	K562	blood:
6	chr15:93350620..93356582-chr15:93455419..93466792,23	MCF-7	breast:
7	chr15:93464070..93466374-chr15:93470199..93472633,2	MCF-7	breast:
8	chr15:93347140..93350047-chr15:93463095..93464830,2	K562	blood:
9	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:
10	chr15:93351614..93354047-chr15:93463305..93465417,2	K562	blood:

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

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs12443243	0.93[ASN][1000 genomes]
rs12908494	0.94[ASN][1000 genomes]
rs1318689	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1406714	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35865218	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3743469	0.85[ASN][1000 genomes]
rs3826036	0.91[ASN][1000 genomes]
rs6497009	0.86[ASN][1000 genomes]
rs6497010	0.85[ASN][1000 genomes]
rs7164668	0.85[ASN][1000 genomes]
rs7168780	0.83[ASN][1000 genomes]
rs7173103	0.95[ASN][1000 genomes]
rs7175134	0.95[ASN][1000 genomes]
rs8024528	0.92[ASN][1000 genomes]
rs8026695	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8035739	0.87[ASN][1000 genomes]
rs961233	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 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	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
8	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
rs28573213	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93455600-93464800	Weak transcription	Fetal Brain Female	brain
2	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr15:93460600-93466400	Genic enhancers	Fetal Intestine Small	intestine
4	chr15:93461200-93464800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:93461200-93465600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr15:93461200-93465600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr15:93461200-93465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
8	chr15:93461200-93466600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
9	chr15:93461200-93467200	Enhancers	Stomach Mucosa	stomach
10	chr15:93461200-93467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr15:93461200-93467600	Weak transcription	Fetal Brain Male	brain
12	chr15:93461200-93467600	Enhancers	Skeletal Muscle Male	skeletal muscle
13	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr15:93461600-93466000	Enhancers	Liver	Liver
15	chr15:93461600-93467600	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:93461600-93471600	Weak transcription	Ovary	ovary
17	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
19	chr15:93461800-93464800	Weak transcription	HUES48 Cell Line	embryonic stem cell
20	chr15:93462000-93464800	Enhancers	Stomach Smooth Muscle	stomach
21	chr15:93462000-93465600	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr15:93462000-93474800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:93462200-93465800	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:93462200-93466400	Enhancers	Fetal Heart	heart
25	chr15:93462600-93466600	Enhancers	Brain Angular Gyrus	brain
26	chr15:93462800-93464600	Enhancers	Rectal Mucosa Donor 31	rectum
27	chr15:93462800-93466000	Genic enhancers	HSMM	muscle
28	chr15:93463000-93464800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
29	chr15:93463000-93464800	Enhancers	Duodenum Mucosa	Duodenum
30	chr15:93463000-93465000	Weak transcription	Fetal Stomach	stomach
31	chr15:93463000-93465000	Enhancers	Monocytes-CD14+_RO01746	blood
32	chr15:93463000-93466000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr15:93463000-93466200	Genic enhancers	HUES6 Cell Line	embryonic stem cell
34	chr15:93463000-93466200	Genic enhancers	K562	blood
35	chr15:93463000-93466400	Genic enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr15:93463000-93466400	Genic enhancers	HUES64 Cell Line	embryonic stem cell
37	chr15:93463000-93466400	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr15:93463000-93466400	Enhancers	Pancreatic Islets	Pancreatic Islet
39	chr15:93463000-93466600	Genic enhancers	HepG2	liver
40	chr15:93463000-93466600	Genic enhancers	Osteobl	bone
41	chr15:93463200-93464800	Genic enhancers	GM12878-XiMat	blood
42	chr15:93463200-93465400	Genic enhancers	iPS-20b Cell Line	embryonic stem cell
43	chr15:93463200-93466200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
44	chr15:93463200-93466600	Enhancers	iPS-15b Cell Line	embryonic stem cell
45	chr15:93463200-93466600	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr15:93463200-93468000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:93463200-93486800	Strong transcription	Dnd41	blood
48	chr15:93463400-93465200	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:93463400-93465800	Enhancers	Rectal Smooth Muscle	rectum
50	chr15:93463400-93465800	Genic enhancers	NH-A	brain

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