Variant report

Variant	rs3764301
Chromosome Location	chr16:12640477-12640478
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHISA9-4	chr16:12640142-12640541	ENSG00000260601.1

Extended variants
information (count: 75 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs1007324	0.83[EUR][1000 genomes]
rs10492794	0.90[EUR][1000 genomes]
rs11640491	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11643978	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11645403	0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11645654	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11645856	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11645899	0.85[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11647147	0.85[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12148951	0.82[EUR][1000 genomes]
rs12149441	0.82[EUR][1000 genomes]
rs1540279	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1614433	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1615250	0.93[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1616112	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1618096	0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1641873	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641877	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641879	0.93[CEU][hapmap];0.88[CHD][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641881	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641889	0.88[CHD][hapmap];0.88[GIH][hapmap];0.89[MEX][hapmap];0.90[ASN][1000 genomes]
rs1641890	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1641893	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17240735	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs17819472	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1794306	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794307	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794308	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794309	0.93[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794310	0.93[CEU][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794312	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1794313	0.88[EUR][1000 genomes]
rs1794315	0.93[CEU][hapmap]
rs1794316	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1970769	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2006159	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2213293	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301217	0.93[CEU][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301218	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2301219	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2856784	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2865230	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902959	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2902961	0.85[CEU][hapmap];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3975365	0.93[CEU][hapmap];0.88[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs4390575	0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4513084	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs55779146	0.82[EUR][1000 genomes]
rs62026884	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62026887	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62026956	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62026957	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7187812	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7188575	0.83[EUR][1000 genomes]
rs7190533	0.82[EUR][1000 genomes]
rs7191878	0.82[EUR][1000 genomes]
rs7195739	0.81[EUR][1000 genomes]
rs7197122	0.82[EUR][1000 genomes]
rs728583	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs728584	1.00[CEU][hapmap]
rs9788839	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1043096	chr16:12013915-12840769	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	nsv571463	chr16:12367791-12783535	Enhancers Weak transcription Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
3	nsv1051242	chr16:12482972-12897243	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv542749	chr16:12482972-12897243	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv1035581	chr16:12516946-12863700	ZNF genes & repeats Weak transcription Enhancers Genic enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
6	nsv1051607	chr16:12522130-13347676	Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
7	nsv542750	chr16:12522130-13347676	Enhancers Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
8	nsv1054084	chr16:12625727-12650247	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
9	nsv431433	chr16:12628409-12654408	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
10	esv1842867	chr16:12632286-12678721	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv1039338	chr16:12632918-12642955	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
12	nsv1040887	chr16:12632918-12650247	Enhancers Weak transcription Active TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	esv2751546	chr16:12635498-12674704	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
14	nsv1040358	chr16:12636982-12650247	Weak transcription Enhancers Flanking Active TSS Genic enhancers Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12613000-12670800	Weak transcription	Pancreas	Pancrea
2	chr16:12625800-12643400	Weak transcription	Gastric	stomach
3	chr16:12627000-12642200	Weak transcription	Right Ventricle	heart
4	chr16:12632800-12641000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr16:12632800-12646600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr16:12632800-12663800	Weak transcription	Aorta	Aorta
7	chr16:12633000-12646600	Weak transcription	Brain Cingulate Gyrus	brain
8	chr16:12633200-12640600	Weak transcription	Stomach Mucosa	stomach
9	chr16:12633200-12640800	Weak transcription	Duodenum Mucosa	Duodenum
10	chr16:12633400-12654400	Weak transcription	Stomach Smooth Muscle	stomach
11	chr16:12634200-12640600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
12	chr16:12635000-12644200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr16:12635400-12640600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr16:12635600-12641000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
15	chr16:12636000-12642600	Flanking Active TSS	GM12878-XiMat	blood
16	chr16:12636400-12640600	Weak transcription	Primary neutrophils fromperipheralblood	blood
17	chr16:12637200-12642200	Enhancers	Spleen	Spleen
18	chr16:12637600-12641800	Weak transcription	Skeletal Muscle Male	skeletal muscle
19	chr16:12637600-12642400	Enhancers	Primary monocytes fromperipheralblood	blood
20	chr16:12637600-12642800	Enhancers	Primary B cells from cord blood	blood
21	chr16:12638200-12641000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr16:12638400-12641200	Enhancers	Brain Substantia Nigra	brain
23	chr16:12638600-12641600	Weak transcription	Fetal Muscle Leg	muscle
24	chr16:12638600-12643000	Enhancers	Primary B cells from peripheral blood	blood
25	chr16:12638600-12644000	Weak transcription	Primary T cells from cord blood	blood
26	chr16:12638800-12641000	Weak transcription	Fetal Muscle Trunk	muscle
27	chr16:12638800-12645400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr16:12639200-12641000	Weak transcription	HSMM	muscle
29	chr16:12639200-12641000	Enhancers	Monocytes-CD14+_RO01746	blood
30	chr16:12639200-12641200	Enhancers	HepG2	liver
31	chr16:12639200-12643000	Enhancers	Esophagus	oesophagus
32	chr16:12639400-12640800	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr16:12639400-12641200	Weak transcription	HSMMtube	muscle
34	chr16:12639400-12645000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr16:12639400-12646800	Weak transcription	Brain Angular Gyrus	brain
36	chr16:12639400-12659000	Weak transcription	Lung	lung
37	chr16:12639600-12640800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr16:12639600-12645800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr16:12639800-12640600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr16:12639800-12640600	Weak transcription	Fetal Thymus	thymus
41	chr16:12639800-12640800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr16:12639800-12641000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr16:12639800-12641000	Weak transcription	Primary T cells fromperipheralblood	blood
44	chr16:12639800-12641600	Weak transcription	Brain Hippocampus Middle	brain
45	chr16:12640000-12641000	Enhancers	NHEK	skin
46	chr16:12640000-12641200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
47	chr16:12640000-12647200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:12640200-12641400	Enhancers	Primary T helper cells PMA-I stimulated	--
49	chr16:12640200-12644200	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr16:12640400-12640600	Weak transcription	Brain Inferior Temporal Lobe	brain

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