Variant report

Variant	rs2273154
Chromosome Location	chr14:35433187-35433188
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	chr14:35430162..35434482-chr14:35434976..35439153,5	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SRP54-3	chr14:35433120-35433246	NONHSAT036352

Extended variants
information (count: 78 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10130069	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10130509	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10130773	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10134907	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10134914	0.98[ASN][1000 genomes]
rs10136059	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10140135	1.00[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10142667	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10142861	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10143485	0.88[ASN][1000 genomes]
rs10144430	0.93[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10145723	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10146407	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10146699	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10147080	0.81[CHB][hapmap]
rs10148691	0.83[ASN][1000 genomes]
rs10150083	0.83[JPT][hapmap]
rs10151273	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs10151720	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1028448	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11156871	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11540758	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12434485	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.84[JPT][hapmap];0.85[MEX][hapmap];0.88[TSI][hapmap]
rs12435454	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12436971	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12588810	0.83[ASN][1000 genomes]
rs12590678	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[CHD][hapmap];0.84[MEX][hapmap];0.88[TSI][hapmap]
rs13379372	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1568200	0.96[ASN][1000 genomes]
rs17091786	0.81[ASN][1000 genomes]
rs17102829	0.84[CHB][hapmap]
rs17102962	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17103042	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2038254	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2254990	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.93[MKK][hapmap];0.96[TSI][hapmap];0.85[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2273157	0.90[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2295103	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2295104	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.85[TSI][hapmap]
rs2383693	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2415257	0.95[CEU][hapmap]
rs28384418	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs28395170	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28404080	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.96[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap];0.83[ASN][1000 genomes]
rs28535942	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28569331	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28577270	0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs28589276	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28870452	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3759548	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3809448	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.92[TSI][hapmap];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3885855	0.81[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs45531432	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4981258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4982234	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.85[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4982235	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4982236	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs60152856	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61100068	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61191004	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7141261	0.95[ASN][1000 genomes]
rs7147571	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs731906	0.93[CEU][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	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
2	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
3	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
4	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	esv1792223	chr14:35428892-35433187	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
15	esv1796704	chr14:35428892-35433187	Strong transcription Weak transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
16	esv1803671	chr14:35428892-35433187	Weak transcription Strong transcription Enhancers	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2273154	SRP54	cis	lymphoblastoid	seeQTL
rs2273154	PPP2R3C	cis	lymphoblastoid	seeQTL
rs2273154	SRP54	cis	multi-tissue	Pritchard

Chromatin state (count:115 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:35401000-35440400	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr14:35411000-35434600	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr14:35411800-35450000	Weak transcription	Brain Angular Gyrus	brain
4	chr14:35413200-35435200	Weak transcription	A549	lung
5	chr14:35413400-35449600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
6	chr14:35413600-35435000	Weak transcription	Duodenum Smooth Muscle	Duodenum
7	chr14:35414000-35435200	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr14:35417400-35449400	Weak transcription	Dnd41	blood
9	chr14:35417600-35433600	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr14:35417800-35436800	Weak transcription	Osteobl	bone
11	chr14:35417800-35438200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr14:35417800-35439200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
13	chr14:35418000-35450600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr14:35418200-35446000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr14:35418800-35449600	Weak transcription	Placenta	Placenta
16	chr14:35419000-35445000	Weak transcription	Pancreas	Pancrea
17	chr14:35419400-35435000	Weak transcription	H1 Cell Line	embryonic stem cell
18	chr14:35419600-35434000	Weak transcription	K562	blood
19	chr14:35419600-35437000	Weak transcription	Left Ventricle	heart
20	chr14:35419600-35449600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:35419800-35435000	Weak transcription	NH-A	brain
22	chr14:35419800-35449600	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr14:35420000-35440000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr14:35420000-35441200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
25	chr14:35420000-35450000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr14:35420000-35450000	Weak transcription	Small Intestine	intestine
27	chr14:35420400-35450200	Weak transcription	Colon Smooth Muscle	Colon
28	chr14:35420800-35440600	Weak transcription	HSMMtube	muscle
29	chr14:35420800-35440600	Weak transcription	NHDF-Ad	bronchial
30	chr14:35421000-35437400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr14:35421200-35440600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr14:35421200-35449600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
33	chr14:35421200-35449600	Weak transcription	Brain Cingulate Gyrus	brain
34	chr14:35421800-35450600	Weak transcription	Esophagus	oesophagus
35	chr14:35422000-35450000	Weak transcription	Brain Substantia Nigra	brain
36	chr14:35423800-35435000	Weak transcription	Rectal Smooth Muscle	rectum
37	chr14:35423800-35443800	Weak transcription	Brain Hippocampus Middle	brain
38	chr14:35423800-35450000	Weak transcription	Colonic Mucosa	Colon
39	chr14:35424000-35437400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr14:35424000-35440600	Weak transcription	NHEK	skin
41	chr14:35424000-35441000	Weak transcription	NHLF	lung
42	chr14:35424000-35449600	Weak transcription	Brain Germinal Matrix	brain
43	chr14:35424000-35449600	Weak transcription	Skeletal Muscle Male	skeletal muscle
44	chr14:35424200-35434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr14:35424400-35437400	Weak transcription	Fetal Lung	lung
46	chr14:35425200-35441000	Weak transcription	Psoas Muscle	Psoas
47	chr14:35425800-35435200	Weak transcription	Duodenum Mucosa	Duodenum
48	chr14:35425800-35435200	Weak transcription	HUVEC	blood vessel
49	chr14:35425800-35435400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr14:35425800-35437600	Weak transcription	Hela-S3	cervix

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