Variant report

Variant	rs6497010
Chromosome Location	chr15:93479636-93479637
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:7)
CpG islands
(count:0)
Chromatin interactive
region (count:9)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:7 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:93479380-93479852	PANC-1	pancreas:	n/a	n/a
2	JUN	chr15:93479404-93479676	HepG2	liver:	n/a	chr15:93479542-93479555 chr15:93479466-93479478
3	POLR2A	chr15:93479296-93479939	U87	brain:	n/a	n/a
4	JUND	chr15:93479395-93479725	HepG2	liver:	n/a	chr15:93479466-93479478
5	POLR2A	chr15:93479048-93479708	HepG2	liver:	n/a	n/a
6	POLR2A	chr15:93478642-93481530	K562	blood:	n/a	n/a
7	POLR2A	chr15:93479332-93479820	PANC-1	pancreas:	n/a	n/a

No data

(count:9 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:93361426..93365022-chr15:93477396..93480784,3	MCF-7	breast:
2	chr15:93343355..93345337-chr15:93477705..93479824,2	MCF-7	breast:
3	chr15:93478680..93480740-chr15:93486712..93488444,2	K562	blood:
4	chr15:93459946..93461504-chr15:93479253..93480891,2	MCF-7	breast:
5	chr15:93472774..93474766-chr15:93477734..93480112,2	K562	blood:
6	chr15:93426509..93428069-chr15:93477933..93480246,2	MCF-7	breast:
7	chr15:93468876..93471818-chr15:93478065..93480821,2	MCF-7	breast:
8	chr15:93479464..93481444-chr15:93486315..93488454,2	MCF-7	breast:
9	chr15:93448445..93451648-chr15:93477513..93481560,4	K562	blood:

No data

Variant related genes	Relation type
CHD2	TF binding region
ENSG00000272888	Chromatin interaction
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 43 )
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];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11074120	0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs11634566	0.88[CEU][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];0.92[CHB][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12438635	0.88[CEU][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594991	0.92[CEU][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908494	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1318689	0.84[CHB][hapmap];0.86[JPT][hapmap];0.88[ASN][1000 genomes]
rs1320819	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.80[YRI][hapmap];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1406714	0.84[CHB][hapmap];0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1881834	0.84[AMR][1000 genomes]
rs1881835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28573213	0.85[ASN][1000 genomes]
rs35865218	0.85[ASN][1000 genomes]
rs3743469	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3826035	0.88[CEU][hapmap];0.86[CHB][hapmap];0.80[JPT][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs3826036	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4327000	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4778052	0.83[CHB][hapmap]
rs6497009	0.89[AFR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164668	1.00[CEU][hapmap];0.86[CHB][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.84[CHB][hapmap];0.91[YRI][hapmap];0.82[AFR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7168780	0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7171151	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7173103	1.00[CEU][hapmap];0.93[CHB][hapmap];0.86[JPT][hapmap];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7175134	0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7176652	1.00[CHB][hapmap];0.86[JPT][hapmap]
rs8024528	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]
rs8026679	0.85[AMR][1000 genomes]
rs8026695	0.84[CHB][hapmap];0.86[JPT][hapmap];0.87[ASN][1000 genomes]
rs8035739	1.00[CEU][hapmap];0.92[CHB][hapmap];0.86[JPT][hapmap];0.87[AFR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs8042395	0.80[JPT][hapmap];0.82[AMR][1000 genomes]
rs8042632	0.80[JPT][hapmap];0.85[AMR][1000 genomes]
rs920389	0.84[CHB][hapmap]
rs9302362	0.82[AMR][1000 genomes]
rs961233	0.86[JPT][hapmap];0.88[ASN][1000 genomes]

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
rs6497010	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	chr15:93457000-93489800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:93461600-93486800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
4	chr15:93463200-93486800	Strong transcription	Dnd41	blood
5	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
6	chr15:93466200-93480800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
8	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
9	chr15:93466200-93489400	Strong transcription	K562	blood
10	chr15:93466400-93480800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
11	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
12	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
13	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
15	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
16	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
17	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
18	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
19	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
20	chr15:93467800-93480000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
21	chr15:93468600-93490400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:93469000-93489800	Strong transcription	Fetal Thymus	thymus
23	chr15:93469600-93484600	Strong transcription	Left Ventricle	heart
24	chr15:93470000-93479800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr15:93470000-93488200	Strong transcription	GM12878-XiMat	blood
26	chr15:93473400-93480200	Strong transcription	Fetal Brain Female	brain
27	chr15:93473800-93490400	Weak transcription	Right Atrium	heart
28	chr15:93474000-93491400	Strong transcription	Fetal Muscle Trunk	muscle
29	chr15:93474200-93484000	Strong transcription	NHLF	lung
30	chr15:93474200-93490600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr15:93474200-93490600	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr15:93474400-93480800	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr15:93474400-93484600	Strong transcription	Fetal Stomach	stomach
34	chr15:93474400-93486200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:93474400-93490000	Strong transcription	Cortex derived primary cultured neurospheres	brain
36	chr15:93474400-93490000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:93474400-93490400	Strong transcription	NH-A	brain
38	chr15:93474400-93490600	Strong transcription	Hela-S3	cervix
39	chr15:93474400-93492200	Strong transcription	Fetal Kidney	kidney
40	chr15:93474800-93480000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
41	chr15:93474800-93480000	Weak transcription	Pancreas	Pancrea
42	chr15:93474800-93481000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr15:93474800-93481400	Strong transcription	Lung	lung
44	chr15:93474800-93486400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr15:93474800-93489800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr15:93474800-93490600	Strong transcription	Fetal Muscle Leg	muscle
47	chr15:93474800-93490800	Strong transcription	HSMM	muscle
48	chr15:93474800-93492200	Strong transcription	HSMMtube	muscle
49	chr15:93474800-93492200	Strong transcription	Osteobl	bone
50	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin

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