Variant report

Variant	rs12904680
Chromosome Location	chr15:93485456-93485457
allele	C/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	chr15:93485138-93488586	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:93481267..93482883-chr15:93484430..93486055,2	K562	blood:
2	chr15:93482816..93485781-chr15:93488823..93491729,2	K562	blood:

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

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10520716	0.92[JPT][hapmap]
rs10520717	0.86[CEU][hapmap];0.86[JPT][hapmap];0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs10520719	0.80[AMR][1000 genomes]
rs11074127	0.82[JPT][hapmap];0.84[AMR][1000 genomes]
rs11630582	0.82[AMR][1000 genomes]
rs11631553	0.83[AMR][1000 genomes]
rs11632522	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11634204	0.86[JPT][hapmap];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11634207	0.80[AMR][1000 genomes]
rs11637047	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11637185	0.85[AMR][1000 genomes]
rs11857145	0.82[CEU][hapmap];0.83[AMR][1000 genomes]
rs12437674	0.86[JPT][hapmap]
rs12443243	0.93[JPT][hapmap]
rs12901950	0.90[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906132	0.82[AMR][1000 genomes]
rs12907579	0.83[AMR][1000 genomes]
rs12915072	0.90[CEU][hapmap];1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12916015	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1318689	0.93[JPT][hapmap]
rs1320819	0.93[JPT][hapmap]
rs1406714	0.92[JPT][hapmap]
rs1534779	0.82[AMR][1000 genomes]
rs17525800	0.82[AMR][1000 genomes]
rs1881835	0.85[JPT][hapmap]
rs2033844	0.82[AMR][1000 genomes]
rs2119010	0.81[CEU][hapmap];0.84[JPT][hapmap];0.84[AMR][1000 genomes]
rs2272459	0.82[AMR][1000 genomes]
rs28540863	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28668136	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs34266454	1.00[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs34498571	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35327372	1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs35477598	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs35596808	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs36048863	0.94[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs3784786	0.82[AMR][1000 genomes]
rs3817597	0.82[CEU][hapmap]
rs3826036	0.86[JPT][hapmap]
rs4327000	0.86[JPT][hapmap]
rs4778052	0.84[JPT][hapmap]
rs4778065	0.81[AMR][1000 genomes]
rs4778067	0.86[AMR][1000 genomes]
rs56358327	0.93[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs66726419	0.84[AMR][1000 genomes]
rs67190144	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7164668	0.86[JPT][hapmap]
rs7167194	0.82[JPT][hapmap]
rs7173103	0.93[JPT][hapmap]
rs72761955	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8026695	0.92[JPT][hapmap]
rs8035739	0.92[JPT][hapmap]
rs920389	0.84[JPT][hapmap]
rs961233	0.92[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
rs12904680	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	chr15:93466200-93488200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:93466200-93488200	Strong transcription	Thymus	Thymus
8	chr15:93466200-93489400	Strong transcription	K562	blood
9	chr15:93466400-93489000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:93466600-93490600	Strong transcription	Fetal Lung	lung
11	chr15:93466800-93490200	Strong transcription	HUES48 Cell Line	embryonic stem cell
12	chr15:93467200-93490200	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr15:93467200-93490600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:93467400-93489200	Strong transcription	Primary B cells from cord blood	blood
15	chr15:93467400-93490000	Strong transcription	H1 Cell Line	embryonic stem cell
16	chr15:93467600-93490400	Strong transcription	H9 Cell Line	embryonic stem cell
17	chr15:93467600-93490600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:93468600-93490400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr15:93469000-93489800	Strong transcription	Fetal Thymus	thymus
20	chr15:93470000-93488200	Strong transcription	GM12878-XiMat	blood
21	chr15:93473800-93490400	Weak transcription	Right Atrium	heart
22	chr15:93474000-93491400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr15:93474200-93490600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr15:93474200-93490600	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr15:93474400-93486200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
26	chr15:93474400-93490000	Strong transcription	Cortex derived primary cultured neurospheres	brain
27	chr15:93474400-93490000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
28	chr15:93474400-93490400	Strong transcription	NH-A	brain
29	chr15:93474400-93490600	Strong transcription	Hela-S3	cervix
30	chr15:93474400-93492200	Strong transcription	Fetal Kidney	kidney
31	chr15:93474800-93486400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr15:93474800-93489800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr15:93474800-93490600	Strong transcription	Fetal Muscle Leg	muscle
34	chr15:93474800-93490800	Strong transcription	HSMM	muscle
35	chr15:93474800-93492200	Strong transcription	HSMMtube	muscle
36	chr15:93474800-93492200	Strong transcription	Osteobl	bone
37	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:93475000-93492600	Strong transcription	NHDF-Ad	bronchial
39	chr15:93475200-93490200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:93475800-93490400	Strong transcription	Adipose Nuclei	Adipose
41	chr15:93475800-93492200	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr15:93476200-93488200	Strong transcription	NHEK	skin
43	chr15:93476200-93490600	Strong transcription	HMEC	breast
44	chr15:93476200-93490800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
45	chr15:93476800-93487600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr15:93476800-93490800	Strong transcription	Primary neutrophils fromperipheralblood	blood
47	chr15:93476800-93492200	Strong transcription	Skeletal Muscle Female	skeletal muscle
48	chr15:93477200-93493000	Strong transcription	Placenta	Placenta
49	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
50	chr15:93477400-93490200	Strong transcription	ES-I3 Cell Line	embryonic stem cell

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