Variant report

Variant	rs8024528
Chromosome Location	chr15:93463631-93463632
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:8)
CpG islands
(count:0)
Chromatin interactive
region (count:11)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:8 , 50 per page) page: 1

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	POLR2A	chr15:93463583-93466834	K562	blood:	n/a	n/a
3	POLR2A	chr15:93463568-93466760	U87	brain:	n/a	n/a
4	POLR2A	chr15:93463008-93472730	K562	blood:	n/a	n/a
5	POLR2A	chr15:93462866-93463633	U87	brain:	n/a	n/a
6	POLR2A	chr15:93463573-93465288	GM12878	blood:	n/a	n/a
7	POLR2A	chr15:93462946-93466287	A549	lung:	n/a	n/a
8	POLR2A	chr15:93462854-93466503	HepG2	liver:	n/a	n/a

No data

(count:11 , 50 per page) page: 1

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	chr15:93459868..93463900-chr15:93464643..93468863,9	K562	blood:
8	chr15:93347140..93350047-chr15:93463095..93464830,2	K562	blood:
9	chr15:93463483..93466768-chr15:93471204..93475396,3	MCF-7	breast:
10	chr15:93461610..93464401-chr15:93531914..93533700,2	K562	blood:
11	chr15:93351614..93354047-chr15:93463305..93465417,2	K562	blood:

No data

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000258922	Chromatin interaction
ENSG00000185442	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10520716	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.87[EUR][1000 genomes]
rs11074120	0.89[YRI][hapmap];0.86[AMR][1000 genomes]
rs11634566	0.87[CEU][hapmap];0.81[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs12438635	0.87[CEU][hapmap];0.80[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12594991	0.91[CEU][hapmap];0.81[EUR][1000 genomes]
rs12908494	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1318689	1.00[CHB][hapmap];0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs1320819	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs1406714	1.00[CHB][hapmap];0.80[JPT][hapmap];0.90[ASN][1000 genomes]
rs1881834	0.83[AMR][1000 genomes]
rs1881835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28573213	0.92[ASN][1000 genomes]
rs35865218	0.80[ASN][1000 genomes]
rs3743469	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3826035	0.87[CEU][hapmap];0.80[JPT][hapmap]
rs3826036	1.00[CEU][hapmap];0.92[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4327000	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs4778052	0.82[CHB][hapmap];0.80[JPT][hapmap]
rs6497009	0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6497010	1.00[CEU][hapmap];0.83[CHB][hapmap];0.90[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164668	1.00[CEU][hapmap];0.85[CHB][hapmap];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs7168780	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7171151	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7173103	1.00[CEU][hapmap];0.92[CHB][hapmap];0.81[JPT][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7175134	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7176652	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs8026679	0.89[AMR][1000 genomes]
rs8026695	1.00[CHB][hapmap];0.80[JPT][hapmap];0.89[ASN][1000 genomes]
rs8035739	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8042395	0.81[AMR][1000 genomes]
rs8042632	0.89[YRI][hapmap];0.89[AMR][1000 genomes]
rs920389	0.83[CHB][hapmap];0.80[JPT][hapmap]
rs9302362	0.81[AMR][1000 genomes]
rs961233	0.92[CHB][hapmap];0.80[JPT][hapmap];0.90[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
rs8024528	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	chr15:93451800-93464000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr15:93454000-93464000	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:93455600-93464400	Weak transcription	Fetal Muscle Trunk	muscle
4	chr15:93455600-93464800	Weak transcription	Fetal Brain Female	brain
5	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr15:93457200-93464000	Weak transcription	Gastric	stomach
7	chr15:93457800-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr15:93460000-93464000	Weak transcription	Right Ventricle	heart
9	chr15:93460000-93464200	Weak transcription	Esophagus	oesophagus
10	chr15:93460000-93464200	Weak transcription	Spleen	Spleen
11	chr15:93460600-93466400	Genic enhancers	Fetal Intestine Small	intestine
12	chr15:93460800-93464000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:93460800-93464000	Weak transcription	Pancreas	Pancrea
14	chr15:93460800-93464200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr15:93460800-93464400	Weak transcription	Lung	lung
16	chr15:93461000-93464000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr15:93461200-93463800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr15:93461200-93464000	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr15:93461200-93464000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr15:93461200-93464000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:93461200-93464200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:93461200-93464200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr15:93461200-93464800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
24	chr15:93461200-93465600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
25	chr15:93461200-93465600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
26	chr15:93461200-93465800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
27	chr15:93461200-93466600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
28	chr15:93461200-93467200	Enhancers	Stomach Mucosa	stomach
29	chr15:93461200-93467400	Enhancers	Primary T helper naive cells from peripheral blood	blood
30	chr15:93461200-93467600	Weak transcription	Fetal Brain Male	brain
31	chr15:93461200-93467600	Enhancers	Skeletal Muscle Male	skeletal muscle
32	chr15:93461200-93471600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr15:93461400-93464000	Weak transcription	Placenta	Placenta
34	chr15:93461400-93464200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:93461400-93464400	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
36	chr15:93461600-93464200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:93461600-93464200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr15:93461600-93464200	Weak transcription	Right Atrium	heart
39	chr15:93461600-93464200	Enhancers	Skeletal Muscle Female	skeletal muscle
40	chr15:93461600-93464400	Weak transcription	Thymus	Thymus
41	chr15:93461600-93466000	Enhancers	Liver	Liver
42	chr15:93461600-93467600	Enhancers	Brain Cingulate Gyrus	brain
43	chr15:93461600-93471600	Weak transcription	Ovary	ovary
44	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:93461800-93463800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:93461800-93464200	Weak transcription	Primary hematopoietic stem cells	blood
48	chr15:93461800-93464400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:93461800-93464800	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr15:93462000-93463800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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