Variant report

Variant	rs1805725
Chromosome Location	chr12:9097933-9097934
allele	G/T
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	chr12:9097648-9098209	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr12:9097655-9098423	H1-hESC	embryonic stem cell:	n/a	n/a
3	POLR2A	chr12:9097793-9098027	H1-hESC	embryonic stem cell:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:9085152..9087931-chr12:9094994..9098809,4	K562	blood:
2	chr12:9085152..9087425-chr12:9095080..9098809,3	K562	blood:
3	chr12:9096830..9100498-chr12:9102068..9104762,4	K562	blood:

Variant related genes	Relation type
M6PR	TF binding region
KLRG1	TF binding region
ENSG00000111752	Chromatin interaction
ENSG00000139187	Chromatin interaction
ENSG00000003056	Chromatin interaction

Extended variants
information (count: 71 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10129061	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10400516	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10400563	0.83[CHB][hapmap];0.83[CHD][hapmap]
rs1049925	0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs10743568	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10771238	0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10842660	0.82[JPT][hapmap]
rs11048190	0.89[ASN][1000 genomes]
rs11048195	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs11048264	0.86[ASN][1000 genomes]
rs11048337	0.91[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11048338	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs11048344	0.88[ASN][1000 genomes]
rs11048345	0.88[ASN][1000 genomes]
rs11048434	0.87[JPT][hapmap]
rs1121401	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11614202	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12371786	0.85[ASN][1000 genomes]
rs12422905	0.82[ASN][1000 genomes]
rs12423746	0.88[ASN][1000 genomes]
rs12423817	0.88[ASN][1000 genomes]
rs12424026	0.88[ASN][1000 genomes]
rs12812913	0.88[ASN][1000 genomes]
rs12821842	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12823100	0.95[CHB][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs12824212	0.87[JPT][hapmap]
rs12833375	0.88[ASN][1000 genomes]
rs1476911	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1805248	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805677	0.87[JPT][hapmap]
rs1805719	0.87[JPT][hapmap]
rs1805721	0.83[JPT][hapmap]
rs1805722	0.83[JPT][hapmap]
rs1805723	0.83[JPT][hapmap]
rs1805724	0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs1805727	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1805732	0.91[CHB][hapmap];0.91[JPT][hapmap];0.85[ASN][1000 genomes]
rs1805733	0.91[CHB][hapmap];0.82[CHD][hapmap];0.91[JPT][hapmap];0.86[ASN][1000 genomes]
rs1805735	1.00[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1805736	0.82[JPT][hapmap]
rs1805754	0.81[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.85[GIH][hapmap];0.88[ASN][1000 genomes]
rs1805761	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs1805765	0.82[CHB][hapmap];0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs2041624	0.88[ASN][1000 genomes]
rs2041625	0.88[ASN][1000 genomes]
rs2080116	0.83[JPT][hapmap]
rs2159961	0.81[JPT][hapmap]
rs2284349	0.90[YRI][hapmap]
rs2377671	0.88[ASN][1000 genomes]
rs2377672	0.87[ASN][1000 genomes]
rs2377673	0.88[ASN][1000 genomes]
rs2377674	0.88[ASN][1000 genomes]
rs2377676	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34798934	0.88[ASN][1000 genomes]
rs4309200	0.95[CHB][hapmap];0.82[CHD][hapmap];0.87[JPT][hapmap];0.88[ASN][1000 genomes]
rs4639983	0.93[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4883201	0.85[GIH][hapmap]
rs4883203	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6832	0.95[CHB][hapmap];0.82[CHD][hapmap];0.95[JPT][hapmap]
rs7132930	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs7300767	0.88[ASN][1000 genomes]
rs7301381	0.85[ASN][1000 genomes]
rs7309922	0.84[ASN][1000 genomes]
rs7315055	0.83[ASN][1000 genomes]
rs7957321	0.88[ASN][1000 genomes]
rs7961355	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7974486	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs887782	0.92[CEU][hapmap];0.97[GIH][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs933462	0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs987917	0.81[CEU][hapmap];1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv832327	chr12:9081779-9246220	Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1805725	M6PR	cis	lung	GTEx
rs1805725	CD163	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:9068200-9100000	Weak transcription	Stomach Mucosa	stomach
2	chr12:9071400-9099400	Strong transcription	HUES48 Cell Line	embryonic stem cell
3	chr12:9071600-9100000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
4	chr12:9073800-9099800	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr12:9087000-9101200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
6	chr12:9091000-9099000	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr12:9091600-9101200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr12:9093600-9099200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr12:9093600-9099200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr12:9093600-9099600	Strong transcription	HUES6 Cell Line	embryonic stem cell
11	chr12:9093800-9098400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
12	chr12:9093800-9098800	Strong transcription	Primary T cells from cord blood	blood
13	chr12:9093800-9099000	Strong transcription	Fetal Intestine Large	intestine
14	chr12:9093800-9099200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
15	chr12:9093800-9099200	Strong transcription	Primary monocytes fromperipheralblood	blood
16	chr12:9093800-9099200	Strong transcription	Primary T helper cells fromperipheralblood	blood
17	chr12:9093800-9099200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr12:9093800-9099200	Strong transcription	Fetal Thymus	thymus
19	chr12:9093800-9099400	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr12:9093800-9099400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
21	chr12:9093800-9099400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr12:9093800-9099400	Strong transcription	Monocytes-CD14+_RO01746	blood
23	chr12:9093800-9099600	Strong transcription	H1 Cell Line	embryonic stem cell
24	chr12:9093800-9099600	Strong transcription	Muscle Satellite Cultured Cells	--
25	chr12:9093800-9099600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
26	chr12:9093800-9099600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr12:9093800-9099600	Strong transcription	A549	lung
28	chr12:9093800-9099800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr12:9094000-9098000	Strong transcription	Primary T killer naive cells fromperipheralblood	blood
30	chr12:9094000-9098200	Strong transcription	Right Ventricle	heart
31	chr12:9094000-9098200	Strong transcription	Skeletal Muscle Male	skeletal muscle
32	chr12:9094000-9098200	Strong transcription	HUVEC	blood vessel
33	chr12:9094000-9098400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr12:9094000-9098400	Strong transcription	Brain Substantia Nigra	brain
35	chr12:9094000-9098600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
36	chr12:9094000-9098600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
37	chr12:9094000-9098600	Strong transcription	Brain Inferior Temporal Lobe	brain
38	chr12:9094000-9098600	Strong transcription	Skeletal Muscle Female	skeletal muscle
39	chr12:9094000-9098600	Strong transcription	HMEC	breast
40	chr12:9094000-9098600	Strong transcription	NHDF-Ad	bronchial
41	chr12:9094000-9098800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
42	chr12:9094000-9098800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr12:9094000-9098800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
44	chr12:9094000-9098800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr12:9094000-9098800	Strong transcription	Primary T helper cells PMA-I stimulated	--
46	chr12:9094000-9098800	Strong transcription	Brain Anterior Caudate	brain
47	chr12:9094000-9098800	Strong transcription	GM12878-XiMat	blood
48	chr12:9094000-9099000	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr12:9094000-9099000	Strong transcription	Primary B cells from peripheral blood	blood
50	chr12:9094000-9099000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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