Variant report

Variant	rs1728678
Chromosome Location	chr2:188166857-188166858
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:188160492..188162802-chr2:188166384..188168217,2	K562	blood:

Extended variants
information (count: 136 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:132)

rs_ID	r²[population]
rs10174456	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10174735	0.81[ASN][1000 genomes]
rs10179705	0.84[ASN][1000 genomes]
rs10181823	0.81[ASN][1000 genomes]
rs10181845	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10191833	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10194145	0.84[ASN][1000 genomes]
rs10194247	0.84[ASN][1000 genomes]
rs10203398	0.84[ASN][1000 genomes]
rs10203781	0.84[ASN][1000 genomes]
rs10931288	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10931289	0.84[ASN][1000 genomes]
rs11685426	0.84[ASN][1000 genomes]
rs11688116	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11688157	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11689123	0.81[ASN][1000 genomes]
rs11691442	0.84[ASN][1000 genomes]
rs11694265	0.84[EUR][1000 genomes]
rs11894589	0.81[ASN][1000 genomes]
rs11897572	0.84[ASN][1000 genomes]
rs11903296	0.84[ASN][1000 genomes]
rs12693471	0.81[ASN][1000 genomes]
rs13013355	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13019491	0.84[ASN][1000 genomes]
rs13392947	0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13409829	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13411274	0.87[EUR][1000 genomes]
rs13418253	0.81[ASN][1000 genomes]
rs13418561	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13424790	0.81[ASN][1000 genomes]
rs13425233	0.81[ASN][1000 genomes]
rs13427277	0.82[EUR][1000 genomes]
rs13430354	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13430665	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1355519	0.84[ASN][1000 genomes]
rs1355520	0.84[ASN][1000 genomes]
rs1398061	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1528233	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1528236	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1540859	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1609268	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1632282	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs16829016	0.84[ASN][1000 genomes]
rs1706246	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1706254	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1706261	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1706262	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1706273	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1706276	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1728680	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1728690	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17367055	0.84[ASN][1000 genomes]
rs17464221	0.84[ASN][1000 genomes]
rs17756804	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1912848	0.84[ASN][1000 genomes]
rs1918902	0.84[EUR][1000 genomes]
rs1983492	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2030976	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2058670	0.84[ASN][1000 genomes]
rs2203117	0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2349315	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs36110670	0.81[ASN][1000 genomes]
rs36146505	0.88[ASN][1000 genomes]
rs3771067	0.84[ASN][1000 genomes]
rs3771078	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3821180	0.84[ASN][1000 genomes]
rs3821184	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4140885	0.81[ASN][1000 genomes]
rs4667160	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59400383	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60343740	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62172510	0.84[EUR][1000 genomes]
rs62172532	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62172533	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6434219	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6719550	0.82[ASN][1000 genomes]
rs67285003	0.84[ASN][1000 genomes]
rs6744012	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6753700	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs696092	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698579	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698582	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698583	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698588	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698590	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs698592	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698593	0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72902495	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7591567	0.84[ASN][1000 genomes]
rs8176580	0.81[ASN][1000 genomes]
rs8176583	0.81[ASN][1000 genomes]
rs8176592	0.81[ASN][1000 genomes]
rs840564	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840567	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840569	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840570	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840571	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840572	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840574	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840576	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840577	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840578	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs840583	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840584	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840585	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840586	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840587	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840588	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840589	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840590	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840591	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs840593	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840595	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840596	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840597	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs840609	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs840610	0.90[ASN][1000 genomes]
rs840611	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs840616	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs858744	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858756	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs858758	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs858759	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs858919	0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs860846	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs860859	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861458	0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs863972	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs865763	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs880890	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs907463	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9288140	0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1728678	CALCRL	cis	Artery Tibial	GTEx

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188163000-188167000	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr2:188163200-188167000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr2:188163200-188167000	Weak transcription	HSMM	muscle
4	chr2:188164600-188167000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
5	chr2:188164800-188167000	Weak transcription	NHDF-Ad	bronchial
6	chr2:188165000-188167200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr2:188165200-188167000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr2:188165200-188167200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:188166400-188167000	Active TSS	Fetal Lung	lung
10	chr2:188166400-188167600	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr2:188166600-188167200	Active TSS	NHLF	lung
12	chr2:188166600-188167800	Enhancers	HUES48 Cell Line	embryonic stem cell
13	chr2:188166800-188167400	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr2:188166800-188167400	Active TSS	Ovary	ovary
15	chr2:188166800-188167400	Flanking Active TSS	HUVEC	blood vessel
16	chr2:188166800-188167600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr2:188166800-188167600	Enhancers	iPS-20b Cell Line	embryonic stem cell
18	chr2:188166800-188167600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr2:188166800-188167600	Active TSS	Adipose Nuclei	Adipose

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