Variant report

Variant	rs12079745
Chromosome Location	chr1:169101060-169101061
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:169075106..169077398-chr1:169100554..169103661,3	MCF-7	breast:
2	chr1:169099064..169101885-chr1:169111160..169113548,2	K562	blood:
3	chr1:169099109..169101213-chr1:169102148..169104233,2	MCF-7	breast:
4	chr1:169092696..169095785-chr1:169096212..169101951,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 180 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:175)

rs_ID	r²[population]
rs10081959	0.82[CHB][hapmap];0.93[JPT][hapmap]
rs10800403	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800406	0.97[ASN][1000 genomes]
rs10800407	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10800410	0.82[ASN][1000 genomes]
rs10800411	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs10800430	1.00[CEU][hapmap]
rs1080267	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs10919065	0.82[CHB][hapmap]
rs10919073	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10919076	0.97[ASN][1000 genomes]
rs10919079	1.00[CEU][hapmap]
rs10919082	0.81[JPT][hapmap];0.90[ASN][1000 genomes]
rs10919083	0.90[ASN][1000 genomes]
rs10919084	0.90[ASN][1000 genomes]
rs10919086	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs10919090	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs10919094	0.82[ASN][1000 genomes]
rs10919100	1.00[CEU][hapmap]
rs1138486	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11801853	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11802117	0.90[ASN][1000 genomes]
rs11802239	1.00[CEU][hapmap]
rs11809180	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12057856	0.90[ASN][1000 genomes]
rs12065030	1.00[CEU][hapmap]
rs12065884	0.90[ASN][1000 genomes]
rs12066676	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12067018	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12067072	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs12070626	0.82[CHB][hapmap];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12071277	0.84[ASN][1000 genomes]
rs12072226	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12072953	0.90[ASN][1000 genomes]
rs12073439	1.00[CEU][hapmap]
rs12074013	1.00[CEU][hapmap]
rs12075832	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs12076469	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs12076510	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12082618	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12082748	1.00[CEU][hapmap]
rs12082810	0.97[ASN][1000 genomes]
rs12083075	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs12083249	1.00[CEU][hapmap]
rs12083287	0.82[CHB][hapmap]
rs12084964	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086104	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12086292	0.84[ASN][1000 genomes]
rs12086983	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12089118	0.97[ASN][1000 genomes]
rs12095171	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12120493	0.90[CHB][hapmap];0.90[ASN][1000 genomes]
rs12124144	0.90[ASN][1000 genomes]
rs12124168	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12124744	0.83[ASN][1000 genomes]
rs12125921	0.90[ASN][1000 genomes]
rs12125985	0.90[ASN][1000 genomes]
rs12126032	0.84[ASN][1000 genomes]
rs12127305	0.84[ASN][1000 genomes]
rs12127613	0.89[ASN][1000 genomes]
rs12129969	0.82[ASN][1000 genomes]
rs12129979	0.88[CHB][hapmap]
rs12130764	0.82[ASN][1000 genomes]
rs12135928	0.97[ASN][1000 genomes]
rs12140967	0.97[ASN][1000 genomes]
rs12143131	0.97[ASN][1000 genomes]
rs12143135	0.85[ASN][1000 genomes]
rs12143965	0.82[CHB][hapmap];0.89[ASN][1000 genomes]
rs12144705	0.86[ASN][1000 genomes]
rs12145939	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12354315	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12561922	1.00[CEU][hapmap]
rs12562404	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12564558	1.00[CEU][hapmap];0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12564596	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12568636	0.82[ASN][1000 genomes]
rs12691502	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12724494	0.81[CHB][hapmap];0.93[JPT][hapmap]
rs12724802	0.82[CHB][hapmap];0.81[JPT][hapmap]
rs12724812	0.90[ASN][1000 genomes]
rs12724863	0.82[ASN][1000 genomes]
rs12728466	0.82[CHB][hapmap];0.86[JPT][hapmap]
rs12734206	0.82[ASN][1000 genomes]
rs12735503	0.90[ASN][1000 genomes]
rs12736110	0.90[ASN][1000 genomes]
rs12736723	0.82[ASN][1000 genomes]
rs12744184	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12744341	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs12744655	0.95[ASN][1000 genomes]
rs12745732	0.84[ASN][1000 genomes]
rs12747242	0.82[CHB][hapmap];0.84[ASN][1000 genomes]
rs12753710	1.00[CEU][hapmap]
rs12755385	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs12756799	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs12758208	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1320965	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1320966	0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1320967	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1320968	0.97[ASN][1000 genomes]
rs1358712	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1419322	0.82[CHB][hapmap];0.87[JPT][hapmap]
rs1419323	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs1419324	0.97[ASN][1000 genomes]
rs1830492	0.80[ASN][1000 genomes]
rs1830494	0.81[ASN][1000 genomes]
rs1830495	0.89[ASN][1000 genomes]
rs2032044	0.84[ASN][1000 genomes]
rs2050119	0.90[ASN][1000 genomes]
rs2143287	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2179492	0.82[ASN][1000 genomes]
rs2420010	0.95[ASN][1000 genomes]
rs2901029	0.82[CHB][hapmap]
rs34250651	0.90[ASN][1000 genomes]
rs34605921	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34645703	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34847919	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35037551	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35631014	0.90[ASN][1000 genomes]
rs35774511	0.90[ASN][1000 genomes]
rs3737681	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3753298	1.00[CEU][hapmap]
rs3766045	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766052	1.00[CEU][hapmap]
rs3766053	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3766054	0.97[ASN][1000 genomes]
rs3766055	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs3766059	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3766060	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3766062	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs3766063	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3766064	1.00[CEU][hapmap]
rs3766065	0.82[ASN][1000 genomes]
rs3766066	0.82[ASN][1000 genomes]
rs3766067	0.82[ASN][1000 genomes]
rs3766069	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs3766070	0.81[CHB][hapmap];0.82[ASN][1000 genomes]
rs3766071	0.82[ASN][1000 genomes]
rs3766082	1.00[CEU][hapmap]
rs3766088	1.00[CEU][hapmap]
rs3820053	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs3820055	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3820056	0.82[CHB][hapmap];0.82[JPT][hapmap];0.89[ASN][1000 genomes]
rs3820057	1.00[CEU][hapmap]
rs4140540	0.82[CHB][hapmap];0.82[ASN][1000 genomes]
rs4656177	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4656651	0.89[CHB][hapmap];0.85[JPT][hapmap]
rs4656653	0.97[ASN][1000 genomes]
rs4656654	0.90[ASN][1000 genomes]
rs4656655	0.90[ASN][1000 genomes]
rs4656656	0.90[ASN][1000 genomes]
rs4656659	0.82[CHB][hapmap];0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs4656660	0.81[CHB][hapmap];0.80[ASN][1000 genomes]
rs61806209	0.88[ASN][1000 genomes]
rs6695177	0.90[ASN][1000 genomes]
rs6695252	0.90[ASN][1000 genomes]
rs67485965	0.90[ASN][1000 genomes]
rs72637225	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs745922	0.97[ASN][1000 genomes]
rs7518554	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs7529937	0.95[ASN][1000 genomes]
rs7541564	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs7541675	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs7541700	0.81[CHB][hapmap];0.90[ASN][1000 genomes]
rs7552484	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs909929	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[ASN][1000 genomes]
rs909930	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs909931	0.82[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs932394	0.82[CHB][hapmap];0.90[ASN][1000 genomes]
rs932395	0.90[ASN][1000 genomes]
rs958581	0.82[CHB][hapmap];0.82[JPT][hapmap];0.90[ASN][1000 genomes]
rs968304	0.82[CHB][hapmap]
rs9887854	0.97[ASN][1000 genomes]
rs9887857	0.91[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs9887903	0.97[ASN][1000 genomes]
rs9887916	0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
2	esv3522071	chr1:168978325-169339044	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
3	esv3522072	chr1:168978325-169339044	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' Weak transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	35 gene(s)	inside rSNPs	diseases
4	nsv831858	chr1:169022383-169179068	Weak transcription Flanking Active TSS Active TSS Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
QT interval	24952745	GWAS catalog

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169079800-169105800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:169085400-169102200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:169086200-169102000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
4	chr1:169086200-169102000	Weak transcription	GM12878-XiMat	blood
5	chr1:169086200-169102400	Weak transcription	Monocytes-CD14+_RO01746	blood
6	chr1:169086600-169103200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr1:169086600-169103400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:169089600-169101600	Genic enhancers	A549	lung
9	chr1:169089600-169103400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:169090000-169103800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:169090400-169103200	Strong transcription	Sigmoid Colon	Sigmoid Colon
12	chr1:169091000-169102200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr1:169091000-169102200	Strong transcription	HepG2	liver
14	chr1:169091000-169102800	Strong transcription	Hela-S3	cervix
15	chr1:169091200-169124600	Weak transcription	NHLF	lung
16	chr1:169091400-169102200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr1:169091400-169103200	Strong transcription	Liver	Liver
18	chr1:169091400-169103400	Strong transcription	Duodenum Mucosa	Duodenum
19	chr1:169091600-169101200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr1:169091600-169102000	Weak transcription	Pancreas	Pancrea
21	chr1:169091600-169110000	Weak transcription	Spleen	Spleen
22	chr1:169091600-169120400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr1:169091600-169120600	Weak transcription	Lung	lung
24	chr1:169091800-169104200	Strong transcription	Rectal Mucosa Donor 31	rectum
25	chr1:169091800-169137600	Weak transcription	Esophagus	oesophagus
26	chr1:169092200-169102400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
27	chr1:169092400-169106200	Weak transcription	Gastric	stomach
28	chr1:169092600-169103600	Strong transcription	Rectal Mucosa Donor 29	rectum
29	chr1:169093200-169103200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr1:169093400-169102000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr1:169093400-169102000	Strong transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:169093400-169102800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr1:169093600-169102200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
34	chr1:169093600-169102400	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr1:169093800-169101600	Strong transcription	iPS-18 Cell Line	embryonic stem cell
36	chr1:169093800-169102200	Strong transcription	HUES6 Cell Line	embryonic stem cell
37	chr1:169093800-169102400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr1:169093800-169102600	Strong transcription	HUES64 Cell Line	embryonic stem cell
39	chr1:169094000-169101600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
40	chr1:169094600-169104000	Genic enhancers	Brain Hippocampus Middle	brain
41	chr1:169095000-169112600	Weak transcription	Stomach Mucosa	stomach
42	chr1:169095600-169101200	Strong transcription	H9 Cell Line	embryonic stem cell
43	chr1:169095800-169106200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
44	chr1:169096200-169101200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr1:169096600-169137400	Weak transcription	Fetal Stomach	stomach
46	chr1:169096800-169101200	Strong transcription	Brain Germinal Matrix	brain
47	chr1:169096800-169108600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr1:169097000-169130000	Weak transcription	Ovary	ovary
49	chr1:169097400-169102000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
50	chr1:169097600-169108200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell

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