Variant report

Variant	rs1320819
Chromosome Location	chr15:93487854-93487855
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:93478680..93480740-chr15:93486712..93488444,2	K562	blood:
2	chr15:93450697..93453423-chr15:93486225..93488488,2	K562	blood:
3	chr15:93487564..93489597-chr15:93495946..93498208,2	MCF-7	breast:
4	chr15:93479464..93481444-chr15:93486315..93488454,2	MCF-7	breast:
5	chr15:93487362..93489198-chr15:93492112..93493697,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000173575	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs10520716	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10520719	0.86[JPT][hapmap]
rs11074120	0.81[JPT][hapmap]
rs11630582	0.86[JPT][hapmap]
rs11634207	0.86[JPT][hapmap]
rs11634566	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12438635	0.89[CEU][hapmap];0.90[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12594991	0.92[CEU][hapmap];0.91[EUR][1000 genomes]
rs12901950	0.92[JPT][hapmap]
rs12904680	0.93[JPT][hapmap]
rs12905312	0.83[EUR][1000 genomes]
rs12906132	0.86[JPT][hapmap]
rs12907579	0.86[JPT][hapmap]
rs12908494	0.88[EUR][1000 genomes]
rs12916015	0.92[JPT][hapmap]
rs1318689	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1406714	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs1534779	0.86[JPT][hapmap]
rs17525800	0.86[JPT][hapmap]
rs1881835	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2033844	0.86[JPT][hapmap]
rs2272457	0.86[JPT][hapmap]
rs35865218	0.92[ASN][1000 genomes]
rs3743469	0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3784786	0.86[JPT][hapmap]
rs3817597	0.81[JPT][hapmap]
rs3826035	0.89[CEU][hapmap];0.81[JPT][hapmap];0.87[EUR][1000 genomes]
rs3826036	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.88[EUR][1000 genomes]
rs4327000	1.00[CEU][hapmap];0.85[CHB][hapmap];0.93[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4778052	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs4778065	0.85[JPT][hapmap]
rs6497009	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6497010	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]
rs7164668	1.00[CEU][hapmap];0.93[CHB][hapmap];0.93[JPT][hapmap];0.92[YRI][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7167194	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.80[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7168780	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7171151	0.94[AFR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7173103	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7175134	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7176652	0.93[CHB][hapmap];0.86[JPT][hapmap]
rs8024528	1.00[CEU][hapmap];0.92[CHB][hapmap];0.80[JPT][hapmap];0.88[EUR][1000 genomes]
rs8026695	0.92[CHB][hapmap];1.00[JPT][hapmap]
rs8035739	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8042395	0.81[JPT][hapmap]
rs8042632	0.81[JPT][hapmap]
rs920389	0.92[CHB][hapmap];0.92[JPT][hapmap]
rs961233	0.85[CHB][hapmap];1.00[JPT][hapmap]

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
rs1320819	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	chr15:93461600-93489200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:93465400-93488400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
4	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
5	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
6	chr15:93466200-93489400	Strong transcription	K562	blood
7	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
8	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
9	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
10	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
11	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
13	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
14	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
15	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr15:93468600-93490400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr15:93469000-93489800	Strong transcription	Fetal Thymus	thymus
18	chr15:93470000-93488200	Strong transcription	GM12878-XiMat	blood
19	chr15:93473800-93490400	Weak transcription	Right Atrium	heart
20	chr15:93474000-93491400	Strong transcription	Fetal Muscle Trunk	muscle
21	chr15:93474200-93490600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr15:93474200-93490600	Strong transcription	Duodenum Smooth Muscle	Duodenum
23	chr15:93474400-93490000	Strong transcription	Cortex derived primary cultured neurospheres	brain
24	chr15:93474400-93490000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr15:93474400-93490400	Strong transcription	NH-A	brain
26	chr15:93474400-93490600	Strong transcription	Hela-S3	cervix
27	chr15:93474400-93492200	Strong transcription	Fetal Kidney	kidney
28	chr15:93474800-93489800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr15:93474800-93490600	Strong transcription	Fetal Muscle Leg	muscle
30	chr15:93474800-93490800	Strong transcription	HSMM	muscle
31	chr15:93474800-93492200	Strong transcription	HSMMtube	muscle
32	chr15:93474800-93492200	Strong transcription	Osteobl	bone
33	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr15:93475000-93492600	Strong transcription	NHDF-Ad	bronchial
35	chr15:93475200-93490200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr15:93475800-93490400	Strong transcription	Adipose Nuclei	Adipose
37	chr15:93475800-93492200	Strong transcription	Muscle Satellite Cultured Cells	--
38	chr15:93476200-93488200	Strong transcription	NHEK	skin
39	chr15:93476200-93490600	Strong transcription	HMEC	breast
40	chr15:93476200-93490800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
41	chr15:93476800-93490800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:93476800-93492200	Strong transcription	Skeletal Muscle Female	skeletal muscle
43	chr15:93477200-93493000	Strong transcription	Placenta	Placenta
44	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
45	chr15:93477400-93490200	Strong transcription	ES-I3 Cell Line	embryonic stem cell
46	chr15:93477600-93490000	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:93477600-93490200	Strong transcription	Liver	Liver
48	chr15:93477800-93489400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
49	chr15:93477800-93490200	Strong transcription	A549	lung
50	chr15:93478200-93489600	Strong transcription	Primary monocytes fromperipheralblood	blood

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