Variant report

Variant	rs1864230
Chromosome Location	chr16:72460395-72460396
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-DHX38-2	chr16:72459847-72463072	ENSG00000260664.1
2	lnc-PMFBP1-4	chr16:72459384-72461356	ENSG00000261008.2

Extended variants
information (count: 109 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:97)

rs_ID	r²[population]
rs11075927	0.84[AFR][1000 genomes]
rs11075928	0.84[AFR][1000 genomes]
rs11859210	0.95[AFR][1000 genomes]
rs11860511	0.82[AFR][1000 genomes]
rs11861074	0.81[AFR][1000 genomes]
rs12103150	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs13332257	0.91[AFR][1000 genomes]
rs13333424	0.96[AFR][1000 genomes]
rs13333480	0.81[AFR][1000 genomes]
rs13336634	0.86[AFR][1000 genomes]
rs13338269	0.83[AFR][1000 genomes]
rs13338313	0.83[AFR][1000 genomes]
rs13338662	0.85[AFR][1000 genomes]
rs13339625	0.91[AFR][1000 genomes]
rs1429069	0.96[AFR][1000 genomes]
rs1429070	0.98[AFR][1000 genomes]
rs16970828	0.81[AFR][1000 genomes]
rs16970897	0.96[AFR][1000 genomes]
rs16970929	0.96[AFR][1000 genomes]
rs16970996	0.91[AFR][1000 genomes]
rs16971006	0.90[AFR][1000 genomes]
rs2017748	1.00[AFR][1000 genomes]
rs2053234	0.99[AFR][1000 genomes]
rs2107154	0.91[AFR][1000 genomes]
rs2163066	0.85[AFR][1000 genomes]
rs2189339	0.92[AFR][1000 genomes]
rs2336436	0.95[AFR][1000 genomes]
rs28393088	0.82[AFR][1000 genomes]
rs2840012	0.91[AFR][1000 genomes]
rs28459407	0.90[AFR][1000 genomes]
rs28514442	0.91[AFR][1000 genomes]
rs28568963	0.91[AFR][1000 genomes]
rs28569075	0.90[AFR][1000 genomes]
rs28616025	0.90[AFR][1000 genomes]
rs28634932	0.98[AFR][1000 genomes]
rs28679760	0.81[AFR][1000 genomes]
rs28706881	0.81[AFR][1000 genomes]
rs28712432	0.81[AFR][1000 genomes]
rs28888757	0.80[AFR][1000 genomes]
rs35917623	0.84[AFR][1000 genomes]
rs4624185	0.91[AFR][1000 genomes]
rs55777547	0.89[AFR][1000 genomes]
rs57841266	0.97[AFR][1000 genomes]
rs58363387	0.91[AFR][1000 genomes]
rs58819288	0.91[AFR][1000 genomes]
rs61192283	0.86[AFR][1000 genomes]
rs7184113	0.91[AFR][1000 genomes]
rs7185566	0.82[YRI][hapmap]
rs7187532	0.85[AFR][1000 genomes]
rs7188632	0.82[AFR][1000 genomes]
rs7192337	0.86[AFR][1000 genomes]
rs7197250	0.84[AFR][1000 genomes]
rs7198450	0.83[AFR][1000 genomes]
rs7200007	0.83[AFR][1000 genomes]
rs7203819	0.85[AFR][1000 genomes]
rs726887	0.80[AFR][1000 genomes]
rs73583171	0.86[AFR][1000 genomes]
rs73583174	0.86[AFR][1000 genomes]
rs73583188	0.81[AFR][1000 genomes]
rs73587415	0.81[AFR][1000 genomes]
rs73599411	0.95[AFR][1000 genomes]
rs73601423	0.89[AFR][1000 genomes]
rs73601436	0.89[AFR][1000 genomes]
rs8045319	0.84[AFR][1000 genomes]
rs8045813	0.86[AFR][1000 genomes]
rs8046375	0.97[AFR][1000 genomes]
rs8050489	0.90[AFR][1000 genomes]
rs8051123	0.83[AFR][1000 genomes]
rs8051420	1.00[YRI][hapmap];0.90[AFR][1000 genomes]
rs8051595	0.84[AFR][1000 genomes]
rs8051982	0.97[AFR][1000 genomes]
rs8052117	0.82[AFR][1000 genomes]
rs8053288	0.88[AFR][1000 genomes]
rs8053566	0.90[YRI][hapmap];0.85[AFR][1000 genomes]
rs8053837	0.84[AFR][1000 genomes]
rs8057796	0.91[AFR][1000 genomes]
rs8059369	0.91[AFR][1000 genomes]
rs8063144	0.81[AFR][1000 genomes]
rs9302636	0.86[AFR][1000 genomes]
rs9921281	0.81[AFR][1000 genomes]
rs9921921	0.84[AFR][1000 genomes]
rs9922597	0.84[AFR][1000 genomes]
rs9926141	0.88[AFR][1000 genomes]
rs9927677	0.99[AFR][1000 genomes]
rs9928119	0.80[AFR][1000 genomes]
rs9928673	0.90[AFR][1000 genomes]
rs9929864	0.83[AFR][1000 genomes]
rs9930862	0.84[AFR][1000 genomes]
rs9932125	0.91[AFR][1000 genomes]
rs9933062	0.92[AFR][1000 genomes]
rs9934152	0.91[AFR][1000 genomes]
rs9934365	0.81[AFR][1000 genomes]
rs9934457	0.83[AFR][1000 genomes]
rs9935400	0.86[AFR][1000 genomes]
rs9935826	0.86[AFR][1000 genomes]
rs9937525	0.91[AFR][1000 genomes]
rs9937973	0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948468	chr16:71727571-72651914	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS ZNF genes & repeats 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	89 gene(s)	inside rSNPs	diseases
2	nsv1060983	chr16:72074832-72791629	Genic enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
3	nsv1060804	chr16:72078486-72791629	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	58 gene(s)	inside rSNPs	diseases
4	nsv534039	chr16:72287171-72851170	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
5	nsv1063172	chr16:72342110-72537808	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv542947	chr16:72342110-72537808	ZNF genes & repeats Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
7	nsv1067525	chr16:72342110-72602796	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv542948	chr16:72342110-72602796	ZNF genes & repeats Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
9	nsv1057127	chr16:72375524-72509686	Enhancers ZNF genes & repeats Flanking Active TSS Weak transcription Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
10	nsv542949	chr16:72375524-72509686	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
11	nsv1055807	chr16:72418417-72614308	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
12	nsv572956	chr16:72426448-72517014	Weak transcription Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:72443600-72461600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr16:72455200-72462600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr16:72457000-72461600	Weak transcription	HepG2	liver
4	chr16:72457200-72467600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr16:72457600-72460400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr16:72457800-72461200	Weak transcription	Fetal Intestine Small	intestine
7	chr16:72457800-72461400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr16:72457800-72462800	Weak transcription	Primary T cells from cord blood	blood
9	chr16:72458000-72461400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr16:72458600-72460600	Active TSS	NH-A	brain
11	chr16:72458600-72461600	Active TSS	Brain Inferior Temporal Lobe	brain
12	chr16:72458600-72463400	Active TSS	Fetal Brain Female	brain
13	chr16:72458600-72464800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
14	chr16:72458600-72465400	Active TSS	Brain Substantia Nigra	brain
15	chr16:72458600-72465600	Active TSS	Brain Anterior Caudate	brain
16	chr16:72458600-72465800	Active TSS	Brain Angular Gyrus	brain
17	chr16:72458600-72465800	Active TSS	Brain Cingulate Gyrus	brain
18	chr16:72458800-72460400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr16:72458800-72460400	Active TSS	Cortex derived primary cultured neurospheres	brain
20	chr16:72458800-72460600	Strong transcription	Dnd41	blood
21	chr16:72458800-72461400	Weak transcription	Sigmoid Colon	Sigmoid Colon
22	chr16:72458800-72462000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr16:72458800-72462400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr16:72458800-72463200	Active TSS	Brain Germinal Matrix	brain
25	chr16:72458800-72466000	Active TSS	Brain Hippocampus Middle	brain
26	chr16:72459000-72460600	Active TSS	Fetal Brain Male	brain
27	chr16:72459000-72464000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr16:72459000-72464800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
29	chr16:72459600-72460800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr16:72459600-72461200	Strong transcription	Primary B cells from cord blood	blood
31	chr16:72460000-72461800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr16:72460000-72462000	Weak transcription	Primary neutrophils fromperipheralblood	blood
33	chr16:72460000-72462200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
34	chr16:72460000-72462400	Weak transcription	Lung	lung
35	chr16:72460000-72471200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr16:72460200-72460600	Active TSS	Fetal Stomach	stomach
37	chr16:72460200-72462000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr16:72460200-72462600	Weak transcription	Thymus	Thymus

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