Variant report

Variant	rs12760175
Chromosome Location	chr1:46447840-46447841
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 132 )
Associated
traits (count: 16 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10749860	0.89[EUR][1000 genomes]
rs10789475	0.85[EUR][1000 genomes]
rs10789481	0.93[EUR][1000 genomes]
rs10789487	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs10890354	0.87[EUR][1000 genomes]
rs10890361	0.90[EUR][1000 genomes]
rs10890363	0.92[EUR][1000 genomes]
rs10890367	0.94[EUR][1000 genomes]
rs10890369	0.85[EUR][1000 genomes]
rs11211199	0.84[EUR][1000 genomes]
rs11211203	0.87[EUR][1000 genomes]
rs11211208	0.90[EUR][1000 genomes]
rs11211213	0.90[EUR][1000 genomes]
rs11211224	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs11211230	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11211234	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11211241	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11211251	0.82[EUR][1000 genomes]
rs11576305	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11579634	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11589562	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11810993	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12021587	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12032115	0.86[EUR][1000 genomes]
rs12049588	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12139630	0.91[EUR][1000 genomes]
rs12143096	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12144263	0.92[EUR][1000 genomes]
rs12405451	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12409773	0.92[EUR][1000 genomes]
rs12410070	0.91[EUR][1000 genomes]
rs12410071	0.91[EUR][1000 genomes]
rs12561806	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12564541	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12565042	0.84[EUR][1000 genomes]
rs12739439	0.86[EUR][1000 genomes]
rs12740503	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12757810	0.82[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1707340	0.81[EUR][1000 genomes]
rs1768816	0.81[EUR][1000 genomes]
rs2275426	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34102169	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs34175029	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs34325724	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35154628	0.82[EUR][1000 genomes]
rs35743647	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs35945607	0.84[EUR][1000 genomes]
rs4073846	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4076006	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4134386	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4233500	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4376778	0.84[EUR][1000 genomes]
rs4440807	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4457512	0.88[EUR][1000 genomes]
rs4504835	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4545281	0.91[EUR][1000 genomes]
rs4579700	0.86[EUR][1000 genomes]
rs4638056	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4660317	0.88[EUR][1000 genomes]
rs4660319	0.90[EUR][1000 genomes]
rs4660321	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660322	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4660898	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs61102033	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61783200	0.86[EUR][1000 genomes]
rs61783217	0.81[EUR][1000 genomes]
rs61783220	0.90[EUR][1000 genomes]
rs6429582	0.88[EUR][1000 genomes]
rs6656022	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6656992	0.89[EUR][1000 genomes]
rs6660835	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6661593	0.96[EUR][1000 genomes]
rs6661910	0.84[EUR][1000 genomes]
rs6662548	0.84[EUR][1000 genomes]
rs6666743	0.86[EUR][1000 genomes]
rs6668284	0.88[EUR][1000 genomes]
rs6669522	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6672898	0.84[EUR][1000 genomes]
rs6675946	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6677007	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6680211	0.86[EUR][1000 genomes]
rs6680380	0.86[EUR][1000 genomes]
rs6680428	0.82[EUR][1000 genomes]
rs6686134	0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6688365	0.89[EUR][1000 genomes]
rs6694340	0.82[EUR][1000 genomes]
rs6697557	0.87[EUR][1000 genomes]
rs6697843	0.88[EUR][1000 genomes]
rs6698247	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6701614	0.87[EUR][1000 genomes]
rs7515491	0.91[EUR][1000 genomes]
rs7522601	0.84[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7526532	0.86[EUR][1000 genomes]
rs7526678	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs7533956	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7539932	0.87[EUR][1000 genomes]
rs7540325	0.90[EUR][1000 genomes]
rs7540699	0.90[EUR][1000 genomes]
rs7550746	0.89[EUR][1000 genomes]
rs7556436	0.92[EUR][1000 genomes]
rs7556615	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs785464	0.81[EUR][1000 genomes]
rs785471	0.81[EUR][1000 genomes]
rs785472	0.81[EUR][1000 genomes]
rs785473	0.81[EUR][1000 genomes]
rs785479	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9429088	0.82[EUR][1000 genomes]
rs9429183	0.81[EUR][1000 genomes]
rs946529	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9787208	0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932680	chr1:45935520-46686477	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
2	nsv868828	chr1:45953923-46686477	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	232 gene(s)	inside rSNPs	diseases
3	nsv871928	chr1:46024701-46609736	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	123 gene(s)	inside rSNPs	diseases
4	nsv1003049	chr1:46144479-46476149	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	78 gene(s)	inside rSNPs	diseases
5	nsv1008219	chr1:46160098-46493958	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
6	nsv534943	chr1:46160098-46493958	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	42 gene(s)	inside rSNPs	diseases
7	nsv1009355	chr1:46189258-46463012	Active TSS Genic enhancers ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
8	nsv546158	chr1:46216575-46495434	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
9	nsv870911	chr1:46216575-46498375	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	32 gene(s)	inside rSNPs	diseases
10	nsv431268	chr1:46223080-46495480	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
11	nsv1003517	chr1:46244432-46609881	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
12	nsv1007759	chr1:46248667-46493959	Enhancers Weak transcription Strong transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
13	nsv534945	chr1:46248667-46493959	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv916232	chr1:46248686-46493918	Genic enhancers Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
15	nsv1009527	chr1:46286329-46520127	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
16	nsv546161	chr1:46311275-46498375	Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
17	nsv1009474	chr1:46320433-46557734	Weak transcription Flanking Active TSS Enhancers Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
18	nsv1005189	chr1:46335186-46949309	Bivalent/Poised TSS Weak transcription Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
19	nsv534946	chr1:46335186-46949309	ZNF genes & repeats Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
20	esv2761743	chr1:46339858-47026743	Active TSS Weak transcription Bivalent Enhancer Enhancers Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
21	nsv829737	chr1:46352900-46506424	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
22	nsv1000557	chr1:46383876-46591182	Weak transcription Strong transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:16)

SNP	Gene	Cis/trans	Tissue	Source
rs12760175	IPP	Cis_1M	lymphoblastoid	RTeQTL
rs12760175	LOC126661	Cis_1M	lymphoblastoid	RTeQTL
rs12760175	CCDC163P	cis	Thyroid	GTEx
rs12760175	CCDC163P	cis	lung	GTEx
rs12760175	CCDC163P	cis	Artery Tibial	GTEx
rs12760175	MAST2	cis	Artery Aorta	GTEx
rs12760175	CCDC163P	cis	Whole Blood	GTEx
rs12760175	CCDC163P	cis	Esophagus Muscularis	GTEx
rs12760175	CCDC163P	cis	Skin Sun Exposed Lower leg	GTEx
rs12760175	MAST2	cis	Artery Tibial	GTEx
rs12760175	CCDC163P	cis	Stomach	GTEx
rs12760175	CCDC163P	cis	Muscle Skeletal	GTEx
rs12760175	CCDC163P	cis	Nerve Tibial	GTEx
rs12760175	CCDC163P	cis	Esophagus Mucosa	GTEx
rs12760175	CCDC163P	cis	Artery Aorta	GTEx
rs12760175	CCDC163P	cis	Heart Left Ventricle	GTEx

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:46420600-46455800	Weak transcription	HUVEC	blood vessel
2	chr1:46426800-46460000	Weak transcription	Psoas Muscle	Psoas
3	chr1:46435200-46461000	Weak transcription	K562	blood
4	chr1:46436200-46468800	Weak transcription	Stomach Smooth Muscle	stomach
5	chr1:46438200-46459600	Weak transcription	Right Ventricle	heart
6	chr1:46438200-46471400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
7	chr1:46438400-46448400	Weak transcription	Small Intestine	intestine
8	chr1:46438400-46453200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:46438400-46453200	Weak transcription	Primary T cells from cord blood	blood
10	chr1:46438400-46466200	Weak transcription	Left Ventricle	heart
11	chr1:46438600-46463200	Weak transcription	Fetal Heart	heart
12	chr1:46438600-46464000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
13	chr1:46438600-46464800	Weak transcription	Fetal Muscle Trunk	muscle
14	chr1:46438600-46468600	Weak transcription	Fetal Brain Female	brain
15	chr1:46440000-46465000	Weak transcription	Dnd41	blood
16	chr1:46440800-46451800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr1:46441000-46463200	Weak transcription	HSMM	muscle
18	chr1:46441400-46461000	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr1:46441400-46467200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:46445000-46448400	Weak transcription	Fetal Kidney	kidney
21	chr1:46445200-46448800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr1:46445400-46448000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr1:46445400-46448000	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr1:46445400-46453800	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr1:46445600-46448000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:46445600-46467800	Weak transcription	Colonic Mucosa	Colon
27	chr1:46445600-46472000	Weak transcription	A549	lung
28	chr1:46445600-46475600	Weak transcription	Stomach Mucosa	stomach
29	chr1:46445800-46450000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr1:46446400-46460200	Weak transcription	Skeletal Muscle Female	skeletal muscle
31	chr1:46446600-46463200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:46446600-46464000	Weak transcription	Fetal Muscle Leg	muscle
33	chr1:46446600-46464600	Weak transcription	Primary neutrophils fromperipheralblood	blood
34	chr1:46446800-46456200	Weak transcription	GM12878-XiMat	blood
35	chr1:46446800-46463200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr1:46447000-46448000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
37	chr1:46447000-46455400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr1:46447200-46448600	Weak transcription	Fetal Stomach	stomach
39	chr1:46447200-46468400	Weak transcription	Primary hematopoietic stem cells	blood
40	chr1:46447600-46448200	Enhancers	HepG2	liver
41	chr1:46447600-46449400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr1:46447800-46448000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
43	chr1:46447800-46448200	Enhancers	Rectal Mucosa Donor 31	rectum
44	chr1:46447800-46448600	Enhancers	Fetal Intestine Large	intestine
45	chr1:46447800-46448600	Enhancers	Fetal Intestine Small	intestine

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