Variant report

Variant	rs1967723
Chromosome Location	chr14:35409214-35409215
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRP54-5	chr14:35409128-35409702	NR_002937

Extended variants
information (count: 110 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:94)

rs_ID	r²[population]
rs1028449	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs1056879	0.82[JPT][hapmap]
rs11156867	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11156868	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11850317	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11851907	0.81[JPT][hapmap]
rs12050171	0.99[ASN][1000 genomes]
rs12050267	0.99[ASN][1000 genomes]
rs12050390	0.82[ASN][1000 genomes]
rs12050402	0.83[ASN][1000 genomes]
rs12050404	0.84[ASN][1000 genomes]
rs12050447	0.84[ASN][1000 genomes]
rs12161905	0.99[ASN][1000 genomes]
rs12588755	0.98[ASN][1000 genomes]
rs12589278	0.84[CHB][hapmap]
rs12878219	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12880928	0.82[ASN][1000 genomes]
rs12883971	0.96[ASN][1000 genomes]
rs12886251	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12887885	0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs12888272	0.96[ASN][1000 genomes]
rs12890056	0.99[ASN][1000 genomes]
rs12890307	0.81[CHB][hapmap];0.91[ASN][1000 genomes]
rs12891343	0.95[CHB][hapmap];0.95[JPT][hapmap];0.87[ASN][1000 genomes]
rs12892056	0.91[ASN][1000 genomes]
rs12893021	0.92[ASN][1000 genomes]
rs12894365	0.91[ASN][1000 genomes]
rs12894820	0.92[ASN][1000 genomes]
rs12895051	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12897044	0.96[ASN][1000 genomes]
rs17102904	0.92[ASN][1000 genomes]
rs17102923	0.91[ASN][1000 genomes]
rs17102967	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs17102970	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17103005	0.82[JPT][hapmap]
rs1712349	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2143950	0.89[CHB][hapmap];0.95[JPT][hapmap]
rs2179890	0.82[JPT][hapmap]
rs2236167	0.82[JPT][hapmap]
rs2273156	0.84[ASN][1000 genomes]
rs2273158	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs2383688	0.99[ASN][1000 genomes]
rs2383689	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs28373355	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34678475	0.91[ASN][1000 genomes]
rs34927714	0.88[ASN][1000 genomes]
rs35090385	0.92[ASN][1000 genomes]
rs35106382	0.92[ASN][1000 genomes]
rs35337462	0.96[ASN][1000 genomes]
rs35797365	0.91[ASN][1000 genomes]
rs35830406	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35875778	0.88[ASN][1000 genomes]
rs35962127	0.90[ASN][1000 genomes]
rs36008567	0.99[ASN][1000 genomes]
rs36024417	0.90[ASN][1000 genomes]
rs36112862	0.81[ASN][1000 genomes]
rs3809449	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs4573843	0.96[ASN][1000 genomes]
rs4594164	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs56686328	0.84[ASN][1000 genomes]
rs56950244	0.85[ASN][1000 genomes]
rs60803103	0.99[ASN][1000 genomes]
rs712312	0.82[ASN][1000 genomes]
rs7140843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71409556	0.95[ASN][1000 genomes]
rs7141292	0.80[ASN][1000 genomes]
rs71421920	0.92[ASN][1000 genomes]
rs7142489	0.82[JPT][hapmap]
rs7143827	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144423	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs7144617	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs7144646	0.91[ASN][1000 genomes]
rs7145474	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7145608	0.84[ASN][1000 genomes]
rs7153068	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7153550	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap]
rs7156322	0.95[CHB][hapmap];1.00[JPT][hapmap]
rs7158416	0.82[JPT][hapmap]
rs74046408	0.82[ASN][1000 genomes]
rs761505	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs761506	0.97[ASN][1000 genomes]
rs799664	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs8011422	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8014327	0.92[ASN][1000 genomes]
rs8014377	0.95[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap]
rs8016566	0.93[ASN][1000 genomes]
rs8017191	0.82[ASN][1000 genomes]
rs8017225	1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8018114	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[ASN][1000 genomes]
rs8018409	0.99[ASN][1000 genomes]
rs8019179	1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs932473	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs941653	0.89[CHB][hapmap];1.00[JPT][hapmap]
rs9671773	0.82[JPT][hapmap]

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	nsv1041857	chr14:35084889-35417180	Strong transcription Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats 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	45 gene(s)	inside rSNPs	diseases
2	nsv1052162	chr14:35245349-35451187	Weak transcription Strong transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases
3	nsv1053722	chr14:35257458-35465784	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	55 gene(s)	inside rSNPs	diseases
4	nsv1045939	chr14:35311074-35494703	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv456203	chr14:35311272-35512335	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
6	nsv564200	chr14:35311272-35512335	Weak transcription Genic enhancers Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
7	nsv901602	chr14:35367889-35571651	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv901603	chr14:35371697-35435651	Strong transcription Active TSS Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
9	nsv949617	chr14:35379923-35825436	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
10	nsv901604	chr14:35381137-35485748	Flanking Active TSS Weak transcription Active TSS Enhancers Strong transcription Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
11	nsv1043470	chr14:35398522-35754029	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	65 gene(s)	inside rSNPs	diseases
12	nsv542031	chr14:35398522-35754029	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS 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	65 gene(s)	inside rSNPs	diseases
13	esv1802718	chr14:35400075-35429777	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
14	nsv1035925	chr14:35404661-35483420	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
15	nsv976328	chr14:35408827-35409537	Weak transcription Strong transcription	CpG island lncRNA	1 gene(s)	inside rSNPs	diseases
16	nsv901605	chr14:35409214-35512335	Enhancers Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	31 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs1967723	FAM177A1	cis	Muscle Skeletal	GTEx
rs1967723	PPP2R3C	cis	Whole Blood	GTEx
rs1967723	PPP2R3C	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35381400-35412200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr14:35389600-35411400	Weak transcription	Aorta	Aorta
3	chr14:35390000-35412600	Weak transcription	Ovary	ovary
4	chr14:35394600-35424000	Weak transcription	Fetal Lung	lung
5	chr14:35396400-35425200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
6	chr14:35396600-35424800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr14:35397200-35412800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr14:35397800-35420600	Weak transcription	Thymus	Thymus
9	chr14:35398800-35410600	Weak transcription	Fetal Brain Male	brain
10	chr14:35399000-35412200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
11	chr14:35399600-35412200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr14:35400600-35427000	Weak transcription	Primary B cells from cord blood	blood
13	chr14:35400800-35412200	Weak transcription	Adipose Nuclei	Adipose
14	chr14:35401000-35411200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr14:35401000-35421400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr14:35401000-35428800	Weak transcription	GM12878-XiMat	blood
17	chr14:35401000-35440400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr14:35401400-35412200	Weak transcription	Primary T cells fromperipheralblood	blood
19	chr14:35401400-35412200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr14:35401400-35412600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr14:35401400-35428800	Weak transcription	Stomach Mucosa	stomach
22	chr14:35401800-35411600	Weak transcription	Brain Angular Gyrus	brain
23	chr14:35402800-35412600	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr14:35403000-35423800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr14:35403200-35425200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr14:35403600-35425200	Weak transcription	Gastric	stomach
27	chr14:35405800-35412800	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr14:35406200-35412600	Weak transcription	Monocytes-CD14+_RO01746	blood
29	chr14:35407000-35425000	Weak transcription	Spleen	Spleen
30	chr14:35408200-35409800	Strong transcription	HepG2	liver
31	chr14:35408200-35425400	Weak transcription	Stomach Smooth Muscle	stomach
32	chr14:35408800-35409600	Strong transcription	Primary T cells from cord blood	blood
33	chr14:35409000-35419000	Weak transcription	Liver	Liver

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