Variant report

Variant	rs17128440
Chromosome Location	chr14:55861912-55861913
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBPL2-2	chr14:55861658-55861951	NONHSAT037008

Extended variants
information (count: 94 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:88)

rs_ID	r²[population]
rs10131913	0.86[EUR][1000 genomes]
rs10136596	0.95[EUR][1000 genomes]
rs10137307	0.93[EUR][1000 genomes]
rs10139000	0.96[EUR][1000 genomes]
rs10139083	0.82[EUR][1000 genomes]
rs10140869	0.82[EUR][1000 genomes]
rs10141483	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs10142448	0.95[EUR][1000 genomes]
rs10142547	0.84[EUR][1000 genomes]
rs10144345	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10144418	0.93[EUR][1000 genomes]
rs10145203	0.84[EUR][1000 genomes]
rs10147765	0.95[EUR][1000 genomes]
rs10149420	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10150699	0.81[EUR][1000 genomes]
rs10150760	0.95[EUR][1000 genomes]
rs1045002	0.95[EUR][1000 genomes]
rs10467798	0.80[EUR][1000 genomes]
rs1109170	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11547116	0.81[EUR][1000 genomes]
rs11625423	0.85[EUR][1000 genomes]
rs11625968	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11626751	0.94[EUR][1000 genomes]
rs11851169	0.96[EUR][1000 genomes]
rs13379169	0.82[EUR][1000 genomes]
rs1572611	0.92[EUR][1000 genomes]
rs17674463	0.95[EUR][1000 genomes]
rs17674563	0.92[EUR][1000 genomes]
rs17675223	0.84[ASN][1000 genomes]
rs17741542	0.96[EUR][1000 genomes]
rs17741831	0.96[EUR][1000 genomes]
rs1815580	0.92[EUR][1000 genomes]
rs1815581	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2009291	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2016931	0.96[EUR][1000 genomes]
rs2182797	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2209808	0.92[EUR][1000 genomes]
rs2341621	0.81[EUR][1000 genomes]
rs2341622	0.81[EUR][1000 genomes]
rs28428911	0.96[EUR][1000 genomes]
rs28430823	0.96[EUR][1000 genomes]
rs28493647	0.95[EUR][1000 genomes]
rs28568813	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs28612464	0.95[EUR][1000 genomes]
rs28631821	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28660594	0.96[EUR][1000 genomes]
rs28716725	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3742569	0.95[EUR][1000 genomes]
rs3783648	0.92[EUR][1000 genomes]
rs3783650	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3783652	0.96[EUR][1000 genomes]
rs3825616	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4366639	0.85[EUR][1000 genomes]
rs4496026	0.85[EUR][1000 genomes]
rs4597235	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs56270323	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56949365	0.84[EUR][1000 genomes]
rs58260073	0.81[EUR][1000 genomes]
rs59629906	0.81[EUR][1000 genomes]
rs59871474	0.81[EUR][1000 genomes]
rs61210954	0.84[EUR][1000 genomes]
rs6573014	0.82[EUR][1000 genomes]
rs6573017	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6573020	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs66486619	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs66696758	0.81[EUR][1000 genomes]
rs67514154	0.80[EUR][1000 genomes]
rs7144737	0.95[EUR][1000 genomes]
rs7145727	0.90[EUR][1000 genomes]
rs7146748	0.82[EUR][1000 genomes]
rs7146752	0.82[EUR][1000 genomes]
rs7147136	0.92[EUR][1000 genomes]
rs7148171	0.84[EUR][1000 genomes]
rs7153110	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7153612	0.84[EUR][1000 genomes]
rs7153645	0.81[EUR][1000 genomes]
rs7154889	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7158768	0.84[EUR][1000 genomes]
rs7159144	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8006525	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8008119	0.95[EUR][1000 genomes]
rs8013713	0.96[EUR][1000 genomes]
rs8022041	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9323284	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9323285	0.84[ASN][1000 genomes]
rs943590	0.83[EUR][1000 genomes]
rs946059	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs9919926	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039438	chr14:55746585-55886099	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS 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	12 gene(s)	inside rSNPs	diseases
2	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv901959	chr14:55853724-55916225	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	n/a
4	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
5	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription 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	30 gene(s)	inside rSNPs	diseases
6	nsv977470	chr14:55858644-55862313	Strong transcription Weak transcription Genic enhancers Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17128440	RP11-665C16.6	cis	Muscle Skeletal	GTEx

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55808800-55865200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr14:55818200-55877600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:55821400-55865200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr14:55836800-55877800	Weak transcription	Esophagus	oesophagus
5	chr14:55848600-55876600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
6	chr14:55848800-55864600	Weak transcription	Primary neutrophils fromperipheralblood	blood
7	chr14:55848800-55865000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr14:55849200-55876600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr14:55849200-55878000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr14:55849800-55865200	Weak transcription	A549	lung
11	chr14:55850000-55868400	Weak transcription	Right Ventricle	heart
12	chr14:55850800-55865400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:55850800-55865400	Weak transcription	Aorta	Aorta
14	chr14:55851000-55871000	Weak transcription	Pancreas	Pancrea
15	chr14:55852000-55877200	Weak transcription	Placenta Amnion	Placenta Amnion
16	chr14:55852400-55865400	Weak transcription	Colonic Mucosa	Colon
17	chr14:55852800-55865200	Weak transcription	NHEK	skin
18	chr14:55853000-55865200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr14:55853000-55877200	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr14:55853600-55865600	Weak transcription	Fetal Kidney	kidney
21	chr14:55854000-55868400	Weak transcription	Gastric	stomach
22	chr14:55854200-55866400	Weak transcription	Brain Cingulate Gyrus	brain
23	chr14:55854200-55871000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr14:55854400-55865400	Weak transcription	Brain Substantia Nigra	brain
25	chr14:55854800-55878000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr14:55855200-55862200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
27	chr14:55855400-55865200	Weak transcription	HMEC	breast
28	chr14:55855800-55865200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:55855800-55865400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr14:55856000-55865200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr14:55856000-55865200	Weak transcription	Brain Angular Gyrus	brain
32	chr14:55856200-55865200	Weak transcription	NH-A	brain
33	chr14:55856200-55865600	Weak transcription	Colon Smooth Muscle	Colon
34	chr14:55856200-55865800	Weak transcription	HSMMtube	muscle
35	chr14:55856200-55868600	Weak transcription	Psoas Muscle	Psoas
36	chr14:55856200-55876200	Weak transcription	Fetal Brain Male	brain
37	chr14:55856200-55878000	Weak transcription	Spleen	Spleen
38	chr14:55856400-55865400	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr14:55856400-55870400	Weak transcription	GM12878-XiMat	blood
40	chr14:55856400-55876800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr14:55856400-55877600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
42	chr14:55856600-55869800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
43	chr14:55856600-55876600	Weak transcription	Fetal Brain Female	brain
44	chr14:55856800-55862200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr14:55856800-55862800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr14:55856800-55863800	Weak transcription	NHDF-Ad	bronchial
47	chr14:55856800-55864800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr14:55856800-55865000	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr14:55856800-55865000	Weak transcription	NHLF	lung
50	chr14:55856800-55865200	Weak transcription	Osteobl	bone

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