Variant report

Variant	rs6744012
Chromosome Location	chr2:188241519-188241520
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188241492..188244171-chr5:66176765..66178294,2	MCF-7	breast:

Extended variants
information (count: 159 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:149)

rs_ID	r²[population]
rs10174456	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10174735	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10179705	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181823	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10181845	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10191833	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10194145	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194247	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201618	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10203398	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203781	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931283	0.82[EUR][1000 genomes]
rs10931288	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10931289	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11685426	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11688116	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11688157	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11689123	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11691442	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11894589	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11897572	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11903296	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693471	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12987470	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13013355	0.85[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs13019491	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024536	0.83[ASN][1000 genomes]
rs13028645	0.84[ASN][1000 genomes]
rs13392947	0.82[EUR][1000 genomes]
rs13409829	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13411274	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs13418253	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13418561	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13424790	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13425233	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13430354	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13430665	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1355519	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1355520	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398061	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1528233	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1528236	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1540859	0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1609268	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1632282	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16829016	0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706246	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1706254	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1706261	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706262	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706273	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1706276	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1728678	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1728680	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1728690	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17367055	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17464221	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17756804	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1912848	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983492	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2030976	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2058670	0.84[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2203117	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2349315	0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35056802	0.84[ASN][1000 genomes]
rs35870933	0.84[ASN][1000 genomes]
rs36110670	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36146505	0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3771058	0.87[ASN][1000 genomes]
rs3771059	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771061	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3771067	0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3771078	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821180	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821184	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4140885	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4667160	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs59400383	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60343740	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62172532	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62172533	0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6434219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6719550	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67285003	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6753700	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs696092	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698579	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698582	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698583	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698588	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698590	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs698592	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs698593	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72902495	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576066	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586970	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7591567	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598858	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8176498	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176501	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176506	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176525	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176526	0.89[ASN][1000 genomes]
rs8176528	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176541	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176546	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8176580	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8176583	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8176592	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840564	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840567	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840569	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840570	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840571	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840572	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840574	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840576	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840577	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840578	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840583	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840584	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840585	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840586	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840587	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840588	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840589	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840590	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840591	0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs840593	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840595	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840596	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840597	0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840609	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs840610	0.81[AFR][1000 genomes];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs840611	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs840616	0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs858744	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs858756	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs858758	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858759	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs858919	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs860846	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860859	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs861458	0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs863972	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs865763	0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs880890	0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs907463	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288140	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949700	chr2:187713412-188361211	Flanking Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
2	nsv1003061	chr2:187950057-188282330	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv1000617	chr2:187950057-188290511	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv533935	chr2:188089148-188284766	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv834487	chr2:188182556-188353363	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats 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	2 gene(s)	inside rSNPs	diseases
6	nsv875557	chr2:188219052-188370232	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv875558	chr2:188219052-188388311	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv875559	chr2:188219052-188390112	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875560	chr2:188219052-188508011	Weak transcription Strong transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
10	nsv875561	chr2:188226900-188440752	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6744012	CALCRL	cis	Artery Tibial	GTEx

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188204000-188253600	Weak transcription	Fetal Muscle Trunk	muscle
2	chr2:188208800-188250400	Weak transcription	Primary T cells from cord blood	blood
3	chr2:188210800-188248000	Weak transcription	HSMMtube	muscle
4	chr2:188214600-188250800	Weak transcription	Fetal Lung	lung
5	chr2:188214600-188257800	Weak transcription	Ovary	ovary
6	chr2:188223000-188255200	Weak transcription	Fetal Stomach	stomach
7	chr2:188223600-188244400	Weak transcription	Fetal Kidney	kidney
8	chr2:188223800-188242000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr2:188223800-188246400	Weak transcription	Left Ventricle	heart
10	chr2:188223800-188250800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr2:188223800-188257800	Weak transcription	Fetal Muscle Leg	muscle
12	chr2:188225000-188251200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr2:188237200-188251000	Weak transcription	Psoas Muscle	Psoas
14	chr2:188237400-188245600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr2:188237600-188241800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr2:188237600-188246400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr2:188238000-188248000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr2:188238600-188248200	Strong transcription	HUVEC	blood vessel
19	chr2:188239400-188244600	Weak transcription	Primary hematopoietic stem cells	blood
20	chr2:188239600-188243400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr2:188239800-188243000	Weak transcription	Adipose Nuclei	Adipose
22	chr2:188240000-188242800	Weak transcription	Primary monocytes fromperipheralblood	blood
23	chr2:188240400-188257800	Weak transcription	Lung	lung
24	chr2:188240600-188241800	Weak transcription	Osteobl	bone

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links