Variant report

Variant	rs3863439
Chromosome Location	chr16:74470644-74470645
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPIPL2-2	chr16:74468703-74470867	NONHSAT143691

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10871290	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11149709	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11149710	0.99[AFR][1000 genomes];0.90[AMR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11649338	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12447063	0.98[AFR][1000 genomes];0.90[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12449101	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12600126	0.80[JPT][hapmap]
rs2288054	0.82[CEU][hapmap]
rs28607667	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs3760055	0.82[CEU][hapmap]
rs3851726	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3851731	0.80[JPT][hapmap]
rs3863436	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3865166	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4099290	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6564097	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7498574	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8063458	0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:17 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv948443	chr16:73994997-74627711	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1066212	chr16:74068470-74527133	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
3	nsv542954	chr16:74068470-74527133	Flanking Active TSS Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
4	nsv1065964	chr16:74088091-74575604	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
5	nsv916687	chr16:74241238-74896721	Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	102 gene(s)	inside rSNPs	diseases
6	esv2758431	chr16:74334780-74587185	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
7	esv2758656	chr16:74334780-74587185	Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
8	nsv833277	chr16:74334787-74498133	Genic enhancers Weak transcription Strong transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
9	esv2762054	chr16:74337036-74507056	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
10	esv1817585	chr16:74355081-74486997	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	n/a
11	esv1822923	chr16:74362131-74472835	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	n/a
12	esv1829589	chr16:74366364-74496761	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
13	nsv428806	chr16:74394226-74580125	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
14	nsv833278	chr16:74415944-74584123	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
15	nsv1056566	chr16:74456589-74482388	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
16	nsv984353	chr16:74465385-74476602	ZNF genes & repeats Weak transcription Strong transcription Enhancers Bivalent Enhancer Genic enhancers Flanking Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	n/a
17	nsv949374	chr16:74466960-75172358	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs3863439	RFWD3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr16:74455600-74480600	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr16:74460400-74479000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
3	chr16:74463000-74480600	Weak transcription	Brain Germinal Matrix	brain
4	chr16:74463200-74472800	Weak transcription	HSMMtube	muscle
5	chr16:74464600-74475000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr16:74465600-74481600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr16:74465600-74481600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
8	chr16:74465800-74473800	Weak transcription	NHEK	skin
9	chr16:74465800-74474800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr16:74465800-74479600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr16:74465800-74480400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
12	chr16:74465800-74480400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr16:74465800-74480400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr16:74465800-74481000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
15	chr16:74466200-74474400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr16:74466200-74475000	Weak transcription	Brain Anterior Caudate	brain
17	chr16:74466600-74474400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr16:74466600-74483200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr16:74467200-74480800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr16:74467800-74483000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr16:74468200-74498400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
22	chr16:74468800-74483200	Weak transcription	HUES64 Cell Line	embryonic stem cell
23	chr16:74469200-74481400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
24	chr16:74469400-74476200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr16:74469800-74471600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr16:74470000-74474800	Weak transcription	Fetal Muscle Trunk	muscle
27	chr16:74470400-74483000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr16:74470600-74470800	ZNF genes & repeats	Fetal Brain Female	brain
29	chr16:74470600-74472000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr16:74470600-74481800	Weak transcription	Fetal Lung	lung
31	chr16:74470600-74483600	Weak transcription	Brain Cingulate Gyrus	brain
32	chr16:74470600-74484800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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