Variant report

Variant	rs12000541
Chromosome Location	chr9:2413577-2413578
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KIAA0020-1	chr9:2411589-2414510	l_3727_chr9:2411588-2611526_ovary

Extended variants
information (count: 93 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10118478	0.87[ASN][1000 genomes]
rs10732343	0.86[ASN][1000 genomes]
rs10738682	0.88[ASN][1000 genomes]
rs10738683	0.88[ASN][1000 genomes]
rs10757450	0.89[ASN][1000 genomes]
rs10757457	0.88[ASN][1000 genomes]
rs10757459	0.86[ASN][1000 genomes]
rs10811972	0.88[ASN][1000 genomes]
rs10811975	0.89[ASN][1000 genomes]
rs10811994	0.86[ASN][1000 genomes]
rs10811995	0.88[ASN][1000 genomes]
rs10811996	0.88[ASN][1000 genomes]
rs10811997	0.88[ASN][1000 genomes]
rs10811999	0.88[ASN][1000 genomes]
rs10812000	0.88[ASN][1000 genomes]
rs10966115	0.88[ASN][1000 genomes]
rs10966132	0.88[ASN][1000 genomes]
rs10966137	0.88[ASN][1000 genomes]
rs10966139	0.88[ASN][1000 genomes]
rs10966144	0.88[ASN][1000 genomes]
rs11791024	0.88[ASN][1000 genomes]
rs1331830	0.89[ASN][1000 genomes]
rs1331832	0.89[ASN][1000 genomes]
rs1331833	0.89[ASN][1000 genomes]
rs1331834	0.88[ASN][1000 genomes]
rs1331835	0.88[ASN][1000 genomes]
rs1331836	0.98[ASN][1000 genomes]
rs1412184	0.88[ASN][1000 genomes]
rs1412185	0.88[ASN][1000 genomes]
rs1412186	0.88[ASN][1000 genomes]
rs1412188	0.88[ASN][1000 genomes]
rs1576719	0.88[ASN][1000 genomes]
rs1576720	0.89[ASN][1000 genomes]
rs1831548	0.84[ASN][1000 genomes]
rs2104858	0.88[ASN][1000 genomes]
rs2150835	0.85[ASN][1000 genomes]
rs2150836	0.89[ASN][1000 genomes]
rs2183812	0.81[ASN][1000 genomes]
rs2183814	0.89[ASN][1000 genomes]
rs2210399	0.81[ASN][1000 genomes]
rs2376119	0.82[ASN][1000 genomes]
rs2376125	0.89[ASN][1000 genomes]
rs4363251	0.88[ASN][1000 genomes]
rs4363252	0.88[ASN][1000 genomes]
rs4740680	0.88[ASN][1000 genomes]
rs4741692	0.87[ASN][1000 genomes]
rs4741694	0.89[ASN][1000 genomes]
rs4741695	0.86[ASN][1000 genomes]
rs4741699	0.88[ASN][1000 genomes]
rs4741700	0.88[ASN][1000 genomes]
rs4741701	0.88[ASN][1000 genomes]
rs4741703	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4741704	0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6475762	0.88[ASN][1000 genomes]
rs6475766	0.88[ASN][1000 genomes]
rs7019582	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7023637	0.98[ASN][1000 genomes]
rs7025116	0.88[ASN][1000 genomes]
rs7028293	0.88[ASN][1000 genomes]
rs7038869	0.98[ASN][1000 genomes]
rs7041232	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7470470	0.89[ASN][1000 genomes]
rs7847686	0.89[ASN][1000 genomes]
rs7849851	0.89[ASN][1000 genomes]
rs7858528	0.88[ASN][1000 genomes]
rs7858645	0.89[ASN][1000 genomes]
rs866991	0.88[ASN][1000 genomes]
rs872039	0.80[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs959378	0.88[ASN][1000 genomes]
rs959379	0.88[ASN][1000 genomes]
rs959380	0.88[ASN][1000 genomes]
rs959381	0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1020530	chr9:1870197-2658587	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv530929	chr9:1998911-2925112	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	nsv466078	chr9:2218129-2621030	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv613126	chr9:2218129-2621030	Enhancers Weak transcription Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
5	nsv613128	chr9:2253678-2419538	Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv1016677	chr9:2253741-2415423	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
7	nsv529508	chr9:2267812-2684272	Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
8	nsv892063	chr9:2291635-2419538	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
9	nsv892064	chr9:2301610-2447910	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	nsv466080	chr9:2318486-2432800	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
11	nsv613131	chr9:2318486-2432800	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
12	nsv531563	chr9:2324333-2501030	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
13	nsv1021309	chr9:2336185-2506959	Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv892065	chr9:2342366-2424322	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv466081	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv613132	chr9:2353522-2596783	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv892066	chr9:2397564-2589739	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv466082	chr9:2403909-2421273	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv613133	chr9:2403909-2421273	Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv1020479	chr9:2407980-2528346	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
21	nsv539933	chr9:2407980-2528346	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12000541	VLDLR	cis	Artery Tibial	GTEx
rs12000541	RP11-125B21.2	cis	Artery Tibial	GTEx

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:2407800-2418800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr9:2411400-2413600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr9:2411400-2414600	Enhancers	Fetal Kidney	kidney
4	chr9:2411400-2414800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr9:2411600-2413800	Enhancers	iPS-20b Cell Line	embryonic stem cell
6	chr9:2412000-2413600	Enhancers	Cortex derived primary cultured neurospheres	brain
7	chr9:2412000-2414000	Enhancers	Colon Smooth Muscle	Colon
8	chr9:2412000-2414200	Weak transcription	Placenta	Placenta
9	chr9:2412000-2414600	Enhancers	Fetal Muscle Leg	muscle
10	chr9:2412000-2418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr9:2412200-2415600	Enhancers	Placenta Amnion	Placenta Amnion
12	chr9:2412200-2418800	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr9:2412400-2414000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr9:2412400-2414200	Weak transcription	NH-A	brain
15	chr9:2412400-2414400	Enhancers	Fetal Lung	lung
16	chr9:2412400-2417800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr9:2412600-2413800	Enhancers	Rectal Smooth Muscle	rectum
18	chr9:2412600-2420400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr9:2412800-2413800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr9:2412800-2413800	Enhancers	HSMMtube	muscle
21	chr9:2412800-2418200	Weak transcription	Brain Substantia Nigra	brain
22	chr9:2412800-2418400	Weak transcription	Adipose Nuclei	Adipose
23	chr9:2412800-2418400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr9:2413000-2414000	Enhancers	Fetal Stomach	stomach
25	chr9:2413000-2414400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr9:2413000-2418200	Weak transcription	Brain Anterior Caudate	brain
27	chr9:2413000-2418200	Weak transcription	Brain Hippocampus Middle	brain
28	chr9:2413000-2418400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr9:2413000-2418400	Weak transcription	Brain Cingulate Gyrus	brain
30	chr9:2413000-2418600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
31	chr9:2413000-2418600	Weak transcription	Brain Angular Gyrus	brain
32	chr9:2413000-2420400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
33	chr9:2413200-2418400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
34	chr9:2413400-2413800	Enhancers	Ovary	ovary
35	chr9:2413400-2414600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr9:2413400-2415000	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr9:2413400-2415200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
38	chr9:2413400-2416000	Enhancers	Pancreas	Pancrea
39	chr9:2413400-2418200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr9:2413400-2418400	Weak transcription	HUES64 Cell Line	embryonic stem cell
41	chr9:2413400-2418800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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