Variant report

Variant	rs9944311
Chromosome Location	chr16:12460019-12460020
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-RP11-276H1.3.1-2	chr16:12460012-12461326	NONHSAT140620

Extended variants
information (count: 44 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs10518185	0.81[EUR][1000 genomes]
rs11075063	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11859773	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11861545	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11866191	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12102413	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12102589	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12103039	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13336107	1.00[EUR][1000 genomes]
rs13338250	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs168831	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16959254	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs16959258	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17817646	0.88[EUR][1000 genomes]
rs2432631	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2432632	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28469469	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28540294	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561752	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28594525	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28637093	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs31678	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35413938	0.96[EUR][1000 genomes]
rs42672	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57739236	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60161095	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60467313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60642545	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7195034	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8053492	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8061507	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9922297	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9924462	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9928921	0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9929299	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9932979	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9944312	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv833141	chr16:12314613-12487992	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv457411	chr16:12363304-12520199	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv571462	chr16:12363304-12520199	Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	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
6	nsv1045385	chr16:12376389-12517006	Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
7	nsv542748	chr16:12376389-12517006	Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:12410200-12464800	Weak transcription	Gastric	stomach
2	chr16:12428400-12461200	Weak transcription	Thymus	Thymus
3	chr16:12434600-12460200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr16:12435800-12484000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr16:12443600-12470800	Weak transcription	HepG2	liver
6	chr16:12444800-12491400	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr16:12447600-12470000	Weak transcription	Esophagus	oesophagus
8	chr16:12448600-12460400	Weak transcription	Fetal Stomach	stomach
9	chr16:12448600-12471200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr16:12449800-12463000	Strong transcription	Primary B cells from peripheral blood	blood
11	chr16:12450800-12470000	Weak transcription	Fetal Thymus	thymus
12	chr16:12452800-12464200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
13	chr16:12453000-12461000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:12453000-12470600	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr16:12453200-12479000	Weak transcription	Monocytes-CD14+_RO01746	blood
16	chr16:12453400-12467400	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr16:12453400-12469400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
18	chr16:12454400-12469200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr16:12454600-12460800	Weak transcription	GM12878-XiMat	blood
20	chr16:12454600-12470800	Weak transcription	Stomach Smooth Muscle	stomach
21	chr16:12455600-12479400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr16:12456200-12470600	Weak transcription	NHEK	skin
23	chr16:12456800-12478600	Weak transcription	Ovary	ovary
24	chr16:12457000-12492400	Weak transcription	Lung	lung
25	chr16:12457200-12465000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
26	chr16:12457400-12460200	Weak transcription	Brain Cingulate Gyrus	brain
27	chr16:12457400-12460200	Weak transcription	Brain Substantia Nigra	brain
28	chr16:12457400-12462000	Weak transcription	Fetal Heart	heart
29	chr16:12457400-12462200	Weak transcription	Left Ventricle	heart
30	chr16:12457400-12469000	Weak transcription	Brain Angular Gyrus	brain
31	chr16:12457400-12469000	Weak transcription	Brain Anterior Caudate	brain
32	chr16:12457400-12469200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr16:12457400-12497400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr16:12457600-12460200	Weak transcription	Brain Hippocampus Middle	brain
35	chr16:12457600-12464400	Weak transcription	Right Atrium	heart
36	chr16:12457600-12464600	Weak transcription	Adipose Nuclei	Adipose
37	chr16:12457600-12491600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
38	chr16:12457600-12497400	Weak transcription	Spleen	Spleen
39	chr16:12458000-12462000	Strong transcription	Primary T cells from cord blood	blood
40	chr16:12458800-12461000	Weak transcription	Primary B cells from cord blood	blood
41	chr16:12460000-12460400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr16:12460000-12460600	Enhancers	Primary hematopoietic stem cells	blood
43	chr16:12460000-12460600	Enhancers	Cortex derived primary cultured neurospheres	brain
44	chr16:12460000-12460800	Enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr16:12460000-12460800	Enhancers	Brain Germinal Matrix	brain
46	chr16:12460000-12460800	Enhancers	Colon Smooth Muscle	Colon
47	chr16:12460000-12461000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
48	chr16:12460000-12461000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr16:12460000-12461000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr16:12460000-12461000	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin

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