Variant report

Variant	rs34982694
Chromosome Location	chr20:25968143-25968144
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-FAM182A-6	chr20:25968084-25968225	NONHSAT079206

Extended variants
information (count: 50 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11696569	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12624435	0.94[ASN][1000 genomes]
rs13039394	0.93[ASN][1000 genomes]
rs13039873	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2180027	0.89[ASN][1000 genomes]
rs2386804	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs35230476	0.93[ASN][1000 genomes]
rs35778990	0.93[ASN][1000 genomes]
rs4003014	0.90[ASN][1000 genomes]
rs4239752	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813596	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4813597	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4815493	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs58999745	0.94[ASN][1000 genomes]
rs6051065	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6051066	0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6107121	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6107124	0.95[ASN][1000 genomes]
rs6107130	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6115454	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6115458	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6115461	0.94[ASN][1000 genomes]
rs6115475	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6115476	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6132915	0.91[ASN][1000 genomes]
rs6138762	0.91[ASN][1000 genomes]
rs6138767	0.93[ASN][1000 genomes]
rs6138768	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6138777	0.91[ASN][1000 genomes]
rs6138778	0.90[ASN][1000 genomes]
rs66769568	0.91[ASN][1000 genomes]
rs7266039	0.95[ASN][1000 genomes]
rs7274601	0.94[ASN][1000 genomes]
rs74175408	0.91[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	esv2758517	chr20:25701992-26319569	ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
2	esv2758790	chr20:25701992-26319569	Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	50 gene(s)	inside rSNPs	diseases
3	nsv470545	chr20:25715507-26309255	Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
4	nsv1059041	chr20:25832105-26007269	Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
5	nsv1060065	chr20:25832105-26305567	Flanking Bivalent TSS/Enh Enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	44 gene(s)	inside rSNPs	diseases
6	nsv962569	chr20:25876021-26152500	Active TSS Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv585761	chr20:25892571-26299677	Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	41 gene(s)	inside rSNPs	diseases
8	esv3518424	chr20:25911038-26051227	Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv3518425	chr20:25911125-26051144	Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv1060508	chr20:25918612-26305567	ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	40 gene(s)	inside rSNPs	diseases
11	nsv1057970	chr20:25937126-26305567	Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
12	nsv1059447	chr20:25941928-26305567	Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Weak transcription Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
13	nsv9796	chr20:25944188-25979608	Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Bivalent/Poised TSS Weak transcription Bivalent Enhancer	lncRNA	n/a	inside rSNPs	diseases
14	nsv1067411	chr20:25955110-26305567	Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
15	nsv1065198	chr20:25959162-26305567	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	39 gene(s)	inside rSNPs	diseases
16	nsv965898	chr20:25966918-25978277	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs34982694	FAM182B	cis	Skin Sun Exposed Lower leg	GTEx
rs34982694	ABHD12	Cis_1M	lymphoblastoid	RTeQTL
rs34982694	LOC642236	Cis_chr	lymphoblastoid	RTeQTL
rs34982694	FAM182B	cis	Esophagus Muscularis	GTEx

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr20:25965000-25968600	Active TSS	Brain Germinal Matrix	brain
2	chr20:25967000-25968200	Enhancers	Placenta	Placenta
3	chr20:25967600-25968200	Active TSS	Primary T cells from cord blood	blood
4	chr20:25967600-25968200	Flanking Bivalent TSS/Enh	Primary T cells fromperipheralblood	blood
5	chr20:25967600-25968200	Active TSS	Primary hematopoietic stem cells	blood
6	chr20:25967600-25968200	Enhancers	Primary hematopoietic stem cells short term culture	blood
7	chr20:25967600-25968200	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
8	chr20:25967600-25968200	Active TSS	Primary T regulatory cells fromperipheralblood	blood
9	chr20:25967600-25968200	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr20:25967600-25968200	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr20:25967600-25968200	Flanking Active TSS	Adipose Nuclei	Adipose
12	chr20:25967600-25968200	Active TSS	Aorta	Aorta
13	chr20:25967600-25968200	Active TSS	Duodenum Mucosa	Duodenum
14	chr20:25967600-25968200	Bivalent/Poised TSS	Fetal Intestine Small	intestine
15	chr20:25967600-25968200	Active TSS	Fetal Kidney	kidney
16	chr20:25967600-25968200	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
17	chr20:25967600-25968200	Flanking Active TSS	Fetal Stomach	stomach
18	chr20:25967600-25968200	Flanking Active TSS	Right Ventricle	heart
19	chr20:25967600-25968200	Active TSS	GM12878-XiMat	blood
20	chr20:25967600-25968200	Active TSS	K562	blood
21	chr20:25967600-25968200	Active TSS	NHEK	skin
22	chr20:25967600-25968200	Active TSS	Osteobl	bone
23	chr20:25967600-25968400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
24	chr20:25967600-25968400	Active TSS	iPS-20b Cell Line	embryonic stem cell
25	chr20:25967600-25968400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr20:25967600-25968400	Active TSS	Primary T helper naive cells fromperipheralblood	blood
27	chr20:25967600-25968400	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
28	chr20:25967600-25968400	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr20:25967600-25968400	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr20:25967600-25968400	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr20:25967600-25968400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr20:25967600-25968400	Active TSS	Fetal Brain Female	brain
33	chr20:25967600-25968400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
34	chr20:25967600-25968400	Active TSS	Stomach Smooth Muscle	stomach
35	chr20:25967600-25968400	Active TSS	A549	lung
36	chr20:25967600-25968400	Active TSS	HSMM	muscle
37	chr20:25967600-25968400	Active TSS	NH-A	brain
38	chr20:25967600-25968800	Enhancers	Fetal Heart	heart
39	chr20:25967600-25969200	Enhancers	Fetal Brain Male	brain
40	chr20:25967800-25968200	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
41	chr20:25967800-25968200	Bivalent/Poised TSS	HUES48 Cell Line	embryonic stem cell
42	chr20:25967800-25968200	Flanking Bivalent TSS/Enh	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr20:25967800-25968200	Flanking Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr20:25967800-25968200	Bivalent/Poised TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr20:25967800-25968200	Flanking Active TSS	Primary B cells from peripheral blood	blood
46	chr20:25967800-25968200	Active TSS	Primary T helper naive cells from peripheral blood	blood
47	chr20:25967800-25968200	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
48	chr20:25967800-25968200	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
49	chr20:25967800-25968200	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
50	chr20:25967800-25968200	Active TSS	Primary T killer naive cells fromperipheralblood	blood

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