Variant report

Variant	rs7167194
Chromosome Location	chr15:93491550-93491551
allele	A/C
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	chr15:93491111-93491608	K562	blood:	n/a	n/a
2	POLR2A	chr15:93490114-93491661	K562	blood:	n/a	n/a
3	POLR2A	chr15:93490153-93491661	HepG2	liver:	n/a	n/a
4	POLR2A	chr15:93491428-93491613	Hela-S3	cervix:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:93481880..93488025-chr15:93488179..93492236,5	K562	blood:
2	chr15:93479767..93482269-chr15:93490198..93491804,2	K562	blood:
3	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: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10520716	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11634566	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs12437674	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12438635	0.88[CEU][hapmap];0.89[EUR][1000 genomes]
rs12443243	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12594991	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs12901950	0.82[JPT][hapmap]
rs12904680	0.82[JPT][hapmap]
rs12905312	0.82[EUR][1000 genomes]
rs12908494	0.86[EUR][1000 genomes]
rs12916015	0.82[JPT][hapmap]
rs1318689	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs1320819	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]
rs1406714	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs1881835	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35865218	0.91[ASN][1000 genomes]
rs3743469	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3826035	0.88[CEU][hapmap];0.87[EUR][1000 genomes]
rs3826036	1.00[CEU][hapmap];0.92[CHB][hapmap];0.82[JPT][hapmap];0.85[EUR][1000 genomes]
rs4327000	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4778052	0.83[CHB][hapmap];0.91[JPT][hapmap]
rs6497009	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6497010	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]
rs7164668	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[YRI][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7168780	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7171151	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7173103	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7175134	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176652	0.84[CHB][hapmap]
rs8024528	1.00[CEU][hapmap];0.84[CHB][hapmap];0.85[EUR][1000 genomes]
rs8026695	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs8035739	1.00[CEU][hapmap];0.92[CHB][hapmap];0.91[JPT][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs920389	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs961233	0.91[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
rs7167194	CHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:93474400-93492200	Strong transcription	Fetal Kidney	kidney
2	chr15:93474800-93492200	Strong transcription	HSMMtube	muscle
3	chr15:93474800-93492200	Strong transcription	Osteobl	bone
4	chr15:93474800-93501800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr15:93475000-93492600	Strong transcription	NHDF-Ad	bronchial
6	chr15:93475800-93492200	Strong transcription	Muscle Satellite Cultured Cells	--
7	chr15:93476800-93492200	Strong transcription	Skeletal Muscle Female	skeletal muscle
8	chr15:93477200-93493000	Strong transcription	Placenta	Placenta
9	chr15:93477200-93501200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr15:93478600-93503200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:93480400-93493000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr15:93480600-93492200	Strong transcription	Stomach Smooth Muscle	stomach
13	chr15:93480800-93492000	Strong transcription	Colonic Mucosa	Colon
14	chr15:93480800-93492600	Strong transcription	Brain Anterior Caudate	brain
15	chr15:93480800-93494000	Strong transcription	Skeletal Muscle Male	skeletal muscle
16	chr15:93481000-93492800	Strong transcription	Brain Cingulate Gyrus	brain
17	chr15:93482000-93491800	Strong transcription	Fetal Intestine Large	intestine
18	chr15:93482400-93492200	Strong transcription	Brain Inferior Temporal Lobe	brain
19	chr15:93484600-93492600	Strong transcription	Rectal Smooth Muscle	rectum
20	chr15:93485000-93492200	Strong transcription	Fetal Brain Female	brain
21	chr15:93485000-93492600	Strong transcription	Brain Hippocampus Middle	brain
22	chr15:93485000-93492600	Strong transcription	Brain Substantia Nigra	brain
23	chr15:93485000-93494600	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr15:93485200-93492000	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:93486000-93495000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
26	chr15:93486400-93493800	Strong transcription	Fetal Brain Male	brain
27	chr15:93486800-93493200	ZNF genes & repeats	Dnd41	blood
28	chr15:93486800-93494400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:93487600-93492000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
30	chr15:93487600-93494000	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr15:93487600-93500000	Strong transcription	Brain Angular Gyrus	brain
32	chr15:93487800-93492000	Strong transcription	Psoas Muscle	Psoas
33	chr15:93488000-93492000	Strong transcription	Left Ventricle	heart
34	chr15:93488200-93493000	Strong transcription	Lung	lung
35	chr15:93488200-93493200	Strong transcription	Pancreas	Pancrea
36	chr15:93488200-93493600	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
37	chr15:93488200-93494000	ZNF genes & repeats	Primary hematopoietic stem cells	blood
38	chr15:93488200-93494000	ZNF genes & repeats	Thymus	Thymus
39	chr15:93488200-93494000	ZNF genes & repeats	GM12878-XiMat	blood
40	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr15:93488200-93494200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:93488400-93493800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
43	chr15:93489000-93494000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
44	chr15:93489200-93492600	Strong transcription	Right Ventricle	heart
45	chr15:93489200-93493400	ZNF genes & repeats	Primary B cells from cord blood	blood
46	chr15:93489200-93493800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr15:93489200-93493800	Strong transcription	Placenta Amnion	Placenta Amnion
48	chr15:93489200-93494000	Strong transcription	Ovary	ovary
49	chr15:93489400-93493000	ZNF genes & repeats	K562	blood
50	chr15:93489400-93494000	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood

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