Variant report

Variant	rs72909512
Chromosome Location	chr2:189218182-189218183
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:189216542..189219160-chr2:189223081..189224726,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:152)

rs_ID	r²[population]
rs10167709	0.85[EUR][1000 genomes]
rs10168305	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10170220	0.86[EUR][1000 genomes]
rs10174928	0.84[EUR][1000 genomes]
rs10175838	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179836	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179899	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10180000	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10180956	0.84[EUR][1000 genomes]
rs10182377	0.80[EUR][1000 genomes]
rs10184703	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187646	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10187791	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189197	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10189416	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10195059	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10198025	0.86[EUR][1000 genomes]
rs10199261	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10199264	0.81[EUR][1000 genomes]
rs10204144	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10206167	0.86[EUR][1000 genomes]
rs10209424	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10211189	0.86[EUR][1000 genomes]
rs10469734	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10469735	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931355	0.86[EUR][1000 genomes]
rs10931358	0.86[EUR][1000 genomes]
rs1125099	0.86[EUR][1000 genomes]
rs12151691	0.81[EUR][1000 genomes]
rs12329399	0.86[EUR][1000 genomes]
rs12693490	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12693491	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693492	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693493	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693494	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693495	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693497	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12693498	0.86[EUR][1000 genomes]
rs12987018	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987553	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12990374	0.84[EUR][1000 genomes]
rs12995727	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13000379	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13003679	0.93[ASN][1000 genomes]
rs13003972	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13007721	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13021294	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13027220	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13032231	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13382200	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13384413	0.86[EUR][1000 genomes]
rs13385282	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13387350	0.83[EUR][1000 genomes]
rs13388723	0.81[EUR][1000 genomes]
rs13388746	0.81[EUR][1000 genomes]
rs13389879	0.86[EUR][1000 genomes]
rs13390401	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13390524	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394232	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13394421	0.84[EUR][1000 genomes]
rs13394422	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13403228	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13404958	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13412312	0.81[EUR][1000 genomes]
rs13413164	0.93[ASN][1000 genomes]
rs13422246	0.84[EUR][1000 genomes]
rs13422836	0.86[EUR][1000 genomes]
rs13423891	0.81[EUR][1000 genomes]
rs13426709	0.86[EUR][1000 genomes]
rs13427070	0.86[EUR][1000 genomes]
rs13429075	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2004888	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28542209	0.83[EUR][1000 genomes]
rs28572636	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34000922	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34066981	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34135749	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34140900	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34353529	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34358898	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34484855	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34557812	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34575499	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34583514	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34762706	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34762794	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35015018	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35060323	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs35196443	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35325130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35442646	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35536225	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35877064	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36174757	0.86[ASN][1000 genomes]
rs3889818	0.86[ASN][1000 genomes]
rs3924673	0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4128404	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4349309	0.86[EUR][1000 genomes]
rs4381754	0.86[EUR][1000 genomes]
rs4476318	0.84[EUR][1000 genomes]
rs4522565	0.81[EUR][1000 genomes]
rs4535011	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667219	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667220	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667225	0.86[EUR][1000 genomes]
rs4667226	0.86[EUR][1000 genomes]
rs4992742	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4992743	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55693630	0.84[EUR][1000 genomes]
rs55852512	0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56072532	0.84[EUR][1000 genomes]
rs58966470	0.86[EUR][1000 genomes]
rs60796263	0.84[EUR][1000 genomes]
rs6434277	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66923332	0.86[EUR][1000 genomes]
rs66948063	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs66993342	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67086516	0.81[EUR][1000 genomes]
rs67092191	0.81[EUR][1000 genomes]
rs6718697	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720002	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6720983	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6725860	0.86[EUR][1000 genomes]
rs67344766	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6737728	0.86[EUR][1000 genomes]
rs67389016	0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6739162	0.86[EUR][1000 genomes]
rs6743636	0.86[EUR][1000 genomes]
rs6748077	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67621133	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67750782	0.86[EUR][1000 genomes]
rs67798410	0.81[EUR][1000 genomes]
rs67804812	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs67919447	0.81[EUR][1000 genomes]
rs72901602	0.80[AFR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72907672	0.81[EUR][1000 genomes]
rs72909520	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72911423	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73040452	0.86[EUR][1000 genomes]
rs7420700	0.86[EUR][1000 genomes]
rs7571197	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7571494	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579554	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7579610	0.86[EUR][1000 genomes]
rs7593215	0.86[EUR][1000 genomes]
rs7593232	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7607063	0.86[EUR][1000 genomes]
rs9288152	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288153	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288157	0.86[EUR][1000 genomes]
rs9808523	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9808557	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1010394	chr2:188994398-189284092	Flanking Active TSS Enhancers Weak transcription Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	10 gene(s)	inside rSNPs	diseases
2	nsv998395	chr2:189018246-189284092	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	8 gene(s)	inside rSNPs	diseases
3	nsv1010330	chr2:189182307-189265614	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	nsv584053	chr2:189184422-189245515	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv999135	chr2:189184937-189265614	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv584054	chr2:189185726-189233419	Enhancers Weak transcription Flanking Active TSS Strong transcription Bivalent Enhancer ZNF genes & repeats Genic enhancers Active TSS	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv534341	chr2:189200405-189368467	Weak transcription Enhancers Flanking Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:189192200-189225200	Weak transcription	Placenta	Placenta
2	chr2:189194600-189218200	Weak transcription	Gastric	stomach
3	chr2:189199400-189247600	Weak transcription	Aorta	Aorta
4	chr2:189200600-189221600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr2:189205200-189228800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
6	chr2:189205600-189227400	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr2:189206000-189220400	Weak transcription	Fetal Stomach	stomach
8	chr2:189206200-189218200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr2:189206400-189218800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr2:189210200-189224600	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr2:189210400-189225200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr2:189211000-189218200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr2:189211000-189220200	Weak transcription	Fetal Lung	lung
14	chr2:189211000-189221000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr2:189211000-189243400	Weak transcription	HUVEC	blood vessel
16	chr2:189212200-189218200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr2:189212600-189218600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr2:189216800-189224600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr2:189217000-189218200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr2:189217000-189218200	Weak transcription	Pancreas	Pancrea
21	chr2:189217000-189218800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr2:189217000-189223800	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr2:189217000-189234600	Weak transcription	Psoas Muscle	Psoas
24	chr2:189217200-189224400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr2:189217200-189224800	Weak transcription	H9 Cell Line	embryonic stem cell
26	chr2:189217200-189225200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr2:189217400-189219800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr2:189217400-189228800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr2:189218000-189218600	ZNF genes & repeats	A549	lung
30	chr2:189218000-189218800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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