Variant report

Variant	rs11894589
Chromosome Location	chr2:188293391-188293392
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TFPI-1	chr2:188293064-188293616	NONHSAT076019

Extended variants
information (count: 150 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:134)

rs_ID	r²[population]
rs10174456	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10174735	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10179705	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10181823	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10181845	0.81[ASN][1000 genomes]
rs10191833	0.81[ASN][1000 genomes]
rs10194145	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10194247	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10201618	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10203398	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10203781	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10931288	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10931289	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11685426	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11689123	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11691442	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11897572	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11903296	0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12693471	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12987470	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs13019491	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13024536	0.83[ASN][1000 genomes]
rs13028645	0.84[ASN][1000 genomes]
rs13409829	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs13411274	0.82[EUR][1000 genomes]
rs13418253	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13424790	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13425233	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13430354	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13430665	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1355519	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1355520	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1398061	0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1528233	0.90[ASN][1000 genomes]
rs1528236	0.81[ASN][1000 genomes]
rs1609268	0.90[ASN][1000 genomes]
rs1632282	0.90[ASN][1000 genomes]
rs16829016	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1706261	0.90[ASN][1000 genomes]
rs1706262	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1706273	0.81[ASN][1000 genomes]
rs1706276	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1728678	0.81[ASN][1000 genomes]
rs1728680	0.90[ASN][1000 genomes]
rs1728690	0.90[ASN][1000 genomes]
rs17367055	0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs17464221	0.97[ASN][1000 genomes]
rs17756804	0.81[ASN][1000 genomes]
rs1912848	0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1983492	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2030976	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2058670	0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2349315	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35056802	0.84[ASN][1000 genomes]
rs35870933	0.84[ASN][1000 genomes]
rs36110670	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs36146505	0.92[ASN][1000 genomes]
rs3771058	0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3771059	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3771061	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3771067	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3771078	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821180	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3821184	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4140885	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4667160	0.81[ASN][1000 genomes]
rs59400383	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6434219	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6719550	0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs67285003	0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6744012	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6753700	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs696092	0.90[ASN][1000 genomes]
rs698579	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698582	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698583	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698588	0.92[ASN][1000 genomes]
rs698590	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs698592	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs698593	0.89[ASN][1000 genomes]
rs72902495	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7576066	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7586970	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7591567	0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7598858	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8176498	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176501	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176506	0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs8176525	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176526	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8176528	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176541	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8176546	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8176580	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8176583	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8176592	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs840564	0.81[ASN][1000 genomes]
rs840567	0.81[ASN][1000 genomes]
rs840569	0.81[ASN][1000 genomes]
rs840570	0.81[ASN][1000 genomes]
rs840571	0.81[ASN][1000 genomes]
rs840572	0.81[ASN][1000 genomes]
rs840574	0.81[ASN][1000 genomes]
rs840576	0.81[ASN][1000 genomes]
rs840577	0.81[ASN][1000 genomes]
rs840578	0.81[ASN][1000 genomes]
rs840583	0.87[ASN][1000 genomes]
rs840584	0.87[ASN][1000 genomes]
rs840585	0.87[ASN][1000 genomes]
rs840586	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840587	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840588	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840589	0.87[ASN][1000 genomes]
rs840590	0.87[ASN][1000 genomes]
rs840591	0.86[ASN][1000 genomes]
rs840593	0.87[ASN][1000 genomes]
rs840595	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840596	0.87[ASN][1000 genomes]
rs840597	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs840609	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs840610	0.90[ASN][1000 genomes]
rs840611	0.90[ASN][1000 genomes]
rs840616	0.90[ASN][1000 genomes]
rs858744	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858756	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs858758	0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs858759	0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs860846	0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs860859	0.90[ASN][1000 genomes]
rs863972	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs865763	0.81[ASN][1000 genomes]
rs880890	0.87[ASN][1000 genomes]
rs907463	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9288140	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 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	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
3	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
4	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
5	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
6	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
7	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
8	nsv584036	chr2:188256158-188369841	Weak transcription Strong transcription Active TSS Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
9	nsv875562	chr2:188258904-188370232	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv875563	chr2:188258904-188388311	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers 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	4 gene(s)	inside rSNPs	diseases
11	nsv875564	chr2:188258904-188414161	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS 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
12	nsv875565	chr2:188258904-188440752	Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS 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	4 gene(s)	inside rSNPs	diseases
13	nsv875566	chr2:188258904-188626214	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
14	nsv875567	chr2:188258904-188673462	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
15	nsv834488	chr2:188268434-188415496	Enhancers Strong transcription Active TSS Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS 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
16	nsv875568	chr2:188291105-188653806	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11894589	CALCRL	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:188269600-188309800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr2:188269800-188308400	Weak transcription	Primary hematopoietic stem cells	blood
3	chr2:188286600-188304000	Weak transcription	Psoas Muscle	Psoas
4	chr2:188287400-188293800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr2:188287600-188294400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr2:188287800-188294600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr2:188288200-188294400	Genic enhancers	HUVEC	blood vessel
8	chr2:188288200-188294600	Weak transcription	Adipose Nuclei	Adipose
9	chr2:188289200-188294000	Weak transcription	NHEK	skin
10	chr2:188289200-188294400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr2:188289200-188294400	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr2:188289200-188294400	Weak transcription	HMEC	breast
13	chr2:188289200-188294600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr2:188289400-188294000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
15	chr2:188289400-188294000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:188289400-188294000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr2:188289400-188294000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr2:188289400-188294200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr2:188289400-188294200	Weak transcription	HSMMtube	muscle
20	chr2:188289600-188294000	Weak transcription	HSMM	muscle
21	chr2:188289800-188294000	Weak transcription	Muscle Satellite Cultured Cells	--

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