Variant report

Variant	rs1007738
Chromosome Location	chr11:46849360-46849361
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:7)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	STAT3	chr11:46849221-46849388	MCF10A-Er-Src	breast:	n/a	n/a

No data

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

No.	Distal block	Cell Line	Cell type
1	chr11:46846632..46851422-chr11:46865562..46870107,6	K562	blood:
2	chr11:46842194..46845139-chr11:46848231..46850202,2	K562	blood:
3	chr11:46842194..46844369-chr11:46847198..46849731,2	K562	blood:
4	chr11:46844063..46849810-chr11:46866303..46869226,7	MCF-7	breast:
5	chr11:46846447..46850137-chr11:46865562..46868503,5	K562	blood:
6	chr11:46846489..46849488-chr11:46867125..46868928,3	MCF-7	breast:
7	chr11:46846941..46849918-chr11:46939245..46941639,2	MCF-7	breast:

No data

Variant related genes	Relation type
CKAP5	TF binding region
ENSG00000134569	Chromatin interaction
ENSG00000247675	Chromatin interaction
ENSG00000175216	Chromatin interaction

Extended variants
information (count: 103 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:102)

rs_ID	r²[population]
rs10734548	0.88[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10734549	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10742784	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10769205	0.89[GIH][hapmap]
rs10769208	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769211	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10769212	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10769226	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs10838612	0.82[CHB][hapmap];0.91[JPT][hapmap]
rs10838620	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10838624	0.95[ASN][1000 genomes]
rs10838627	0.88[ASN][1000 genomes]
rs10838628	0.88[ASN][1000 genomes]
rs10838629	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10838635	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs10838644	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs11038977	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs11038994	0.95[ASN][1000 genomes]
rs11038999	0.96[ASN][1000 genomes]
rs11039002	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11039014	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11039017	0.88[ASN][1000 genomes]
rs11039018	0.81[ASN][1000 genomes]
rs11600292	0.82[GIH][hapmap];0.88[TSI][hapmap]
rs11602036	0.89[ASN][1000 genomes]
rs12361673	0.89[GIH][hapmap]
rs12575609	0.92[ASN][1000 genomes]
rs12806577	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12807111	0.87[EUR][1000 genomes]
rs13448	0.86[GIH][hapmap]
rs1551744	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1809293	0.95[ASN][1000 genomes]
rs2035068	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2070850	0.86[CHB][hapmap]
rs2070852	0.89[GIH][hapmap];0.88[MEX][hapmap]
rs2290883	0.95[ASN][1000 genomes]
rs2290884	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306026	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2306027	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2306028	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2306033	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2306035	0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2306036	0.81[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.82[ASN][1000 genomes]
rs2306037	1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3136441	0.90[CHB][hapmap];1.00[JPT][hapmap]
rs3136447	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3136457	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs3136460	0.91[CHB][hapmap];1.00[JPT][hapmap]
rs3816614	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3829940	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4075619	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4076557	0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap]
rs4294527	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4394802	0.83[GIH][hapmap];0.81[JPT][hapmap];0.89[TSI][hapmap]
rs4453193	0.90[ASN][1000 genomes]
rs4453194	0.86[ASN][1000 genomes]
rs4469848	0.95[ASN][1000 genomes]
rs4534535	0.90[ASN][1000 genomes]
rs4581406	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs4606447	0.87[GIH][hapmap]
rs4752815	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs4752816	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs4752927	0.91[JPT][hapmap]
rs4752932	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap]
rs4752933	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs4752936	0.95[ASN][1000 genomes]
rs4752940	0.99[ASN][1000 genomes]
rs4752941	0.96[ASN][1000 genomes]
rs4752946	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.95[ASN][1000 genomes]
rs4752947	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs5896	0.91[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap]
rs60258676	0.95[ASN][1000 genomes]
rs6485692	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6485695	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6485696	0.94[GIH][hapmap]
rs6485702	0.91[GIH][hapmap]
rs6485715	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7101374	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7107778	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.96[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7109707	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7118170	0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7119247	0.87[ASN][1000 genomes]
rs7124648	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7126005	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7128650	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7130947	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7480140	0.87[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7480260	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7929294	0.83[ASW][hapmap];0.85[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];0.96[LWK][hapmap];0.87[MEX][hapmap];0.95[MKK][hapmap];0.96[TSI][hapmap];0.95[YRI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7934421	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7935346	0.85[GIH][hapmap];0.89[TSI][hapmap]
rs7938169	0.83[GIH][hapmap];0.89[TSI][hapmap]
rs7940441	0.92[GIH][hapmap];0.82[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.82[EUR][1000 genomes]
rs7940578	0.89[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7940682	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7941252	0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7941894	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7941964	0.91[ASN][1000 genomes]
rs7943866	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7945558	0.89[TSI][hapmap]
rs898604	0.82[ASN][1000 genomes]
rs964551	0.94[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.96[MEX][hapmap];0.97[MKK][hapmap];0.96[TSI][hapmap];0.91[YRI][hapmap];0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[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	nsv430382	chr11:46743135-46849360	Weak transcription Strong transcription Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	12 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Bone mineral density (hip)	19079262	GWAS catalog

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1007738	ACP2	cis	lymphoblastoid	seeQTL

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:46841000-46853400	Weak transcription	Dnd41	blood
2	chr11:46848400-46856800	Weak transcription	Small Intestine	intestine
3	chr11:46848400-46863800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr11:46848400-46866200	Weak transcription	Placenta	Placenta
5	chr11:46848600-46849600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr11:46848600-46850200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr11:46848600-46850200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
8	chr11:46848600-46851200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr11:46848800-46849400	Enhancers	HUES64 Cell Line	embryonic stem cell
10	chr11:46848800-46849600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
11	chr11:46848800-46849600	Enhancers	Cortex derived primary cultured neurospheres	brain
12	chr11:46848800-46849600	Enhancers	Brain Angular Gyrus	brain
13	chr11:46848800-46849600	Enhancers	Skeletal Muscle Male	skeletal muscle
14	chr11:46848800-46850000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr11:46848800-46850000	Weak transcription	Gastric	stomach
16	chr11:46848800-46850000	Enhancers	HUVEC	blood vessel
17	chr11:46848800-46850000	Enhancers	NHLF	lung
18	chr11:46848800-46850200	Enhancers	iPS-20b Cell Line	embryonic stem cell
19	chr11:46848800-46850200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr11:46848800-46850200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
21	chr11:46848800-46850200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
22	chr11:46848800-46850200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
23	chr11:46848800-46850200	Enhancers	Adipose Nuclei	Adipose
24	chr11:46848800-46850200	Enhancers	Brain Anterior Caudate	brain
25	chr11:46848800-46850200	Enhancers	Brain Substantia Nigra	brain
26	chr11:46848800-46850200	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr11:46848800-46850200	Enhancers	HMEC	breast
28	chr11:46848800-46850400	Enhancers	Muscle Satellite Cultured Cells	--
29	chr11:46848800-46850400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr11:46848800-46850400	Enhancers	Osteobl	bone
31	chr11:46848800-46850600	Enhancers	Fetal Heart	heart
32	chr11:46848800-46850600	Enhancers	Stomach Mucosa	stomach
33	chr11:46848800-46851000	Enhancers	Fetal Lung	lung
34	chr11:46848800-46851400	Enhancers	K562	blood
35	chr11:46848800-46854000	Weak transcription	Fetal Intestine Small	intestine
36	chr11:46848800-46854400	Weak transcription	Placenta Amnion	Placenta Amnion
37	chr11:46848800-46857600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr11:46848800-46862200	Weak transcription	Fetal Muscle Trunk	muscle
39	chr11:46848800-46865800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
40	chr11:46849000-46849400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr11:46849000-46849400	Weak transcription	HSMM	muscle
42	chr11:46849000-46849600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
43	chr11:46849000-46849600	Enhancers	Brain Hippocampus Middle	brain
44	chr11:46849000-46849600	Weak transcription	Duodenum Mucosa	Duodenum
45	chr11:46849000-46849800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
46	chr11:46849000-46850000	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr11:46849000-46850000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
48	chr11:46849000-46850000	Weak transcription	Stomach Smooth Muscle	stomach
49	chr11:46849000-46850000	Enhancers	GM12878-XiMat	blood
50	chr11:46849000-46850200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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