Variant report

Variant	rs40561
Chromosome Location	chr19:23541372-23541373
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-AC092329.1-2	chr19:23541232-23541619	NONHSAT063901
2	lnc-AC092329.1-2	chr19:23541232-23541650	NONHSAT063902
3	lnc-AC092329.1-2	chr19:23541232-23541782	NONHSAT063903

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs10415339	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.86[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10417541	0.89[CEU][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1044095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10854068	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11879939	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1821845	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2127370	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2885846	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs293895	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs295413	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs295418	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29983	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs29984	0.98[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29985	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29986	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs29988	0.89[CEU][hapmap];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs29989	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs29990	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs36119092	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs423265	0.83[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs429771	0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs431270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs445825	0.80[AFR][1000 genomes]
rs604495	1.00[CEU][hapmap];0.92[CHB][hapmap];0.89[JPT][hapmap];0.95[YRI][hapmap];0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6511434	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs771701	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv34470	chr19:22922549-23659458	ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
2	esv34907	chr19:22922549-23683097	Weak transcription ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	80 gene(s)	inside rSNPs	diseases
3	nsv9686	chr19:22989454-23653750	Weak transcription Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
4	nsv817826	chr19:23000745-23620632	Active TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	75 gene(s)	inside rSNPs	diseases
5	esv3693269	chr19:23000745-23652839	Weak transcription Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	76 gene(s)	inside rSNPs	diseases
6	esv2758491	chr19:23071299-23940467	ZNF genes & repeats Bivalent/Poised TSS Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	87 gene(s)	inside rSNPs	diseases
7	nsv1065157	chr19:23091826-23812323	Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Enhancers Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
8	nsv543959	chr19:23091826-23812323	Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	83 gene(s)	inside rSNPs	diseases
9	esv3429878	chr19:23246650-23590744	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
10	esv3410568	chr19:23246670-23590714	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
11	esv3433243	chr19:23249108-23585814	Strong transcription Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
12	esv3387823	chr19:23265885-23590028	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	47 gene(s)	inside rSNPs	diseases
13	nsv579034	chr19:23387788-23610784	ZNF genes & repeats Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
14	nsv833790	chr19:23405972-23557520	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
15	esv3332495	chr19:23451842-23598069	Active TSS Strong transcription ZNF genes & repeats Genic enhancers Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
16	esv3319024	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Strong transcription Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
17	esv3319025	chr19:23456003-23598068	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
18	esv3447830	chr19:23465035-23610690	Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	36 gene(s)	inside rSNPs	diseases
19	esv3382338	chr19:23476728-23631356	Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Weak transcription Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
20	esv3323302	chr19:23477342-23648545	ZNF genes & repeats Weak transcription Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
21	esv3523857	chr19:23477614-23632199	ZNF genes & repeats Weak transcription Active TSS Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	34 gene(s)	inside rSNPs	diseases
22	esv3523858	chr19:23477614-23632199	Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	34 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	chr19:23506000-23548400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
2	chr19:23512400-23548400	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr19:23513200-23570400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr19:23524000-23548400	ZNF genes & repeats	Duodenum Mucosa	Duodenum
5	chr19:23524200-23548400	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:23524200-23548400	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr19:23524400-23552200	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
8	chr19:23524400-23570200	ZNF genes & repeats	Liver	Liver
9	chr19:23524600-23546400	ZNF genes & repeats	Fetal Brain Female	brain
10	chr19:23524600-23547400	ZNF genes & repeats	Adipose Nuclei	Adipose
11	chr19:23524600-23547800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
12	chr19:23524600-23570000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
13	chr19:23526000-23541400	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
14	chr19:23526000-23547200	ZNF genes & repeats	Rectal Mucosa Donor 29	rectum
15	chr19:23526400-23547400	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr19:23529400-23556800	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
17	chr19:23536800-23548400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr19:23537000-23548200	ZNF genes & repeats	Fetal Lung	lung
19	chr19:23537200-23541800	ZNF genes & repeats	HUES6 Cell Line	embryonic stem cell
20	chr19:23538200-23541600	ZNF genes & repeats	Dnd41	blood
21	chr19:23538400-23541600	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
22	chr19:23538800-23543400	ZNF genes & repeats	ES-I3 Cell Line	embryonic stem cell
23	chr19:23539400-23544800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr19:23539400-23548200	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
25	chr19:23540000-23541400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr19:23540000-23541800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
27	chr19:23540000-23542200	Weak transcription	Left Ventricle	heart
28	chr19:23540000-23545600	Weak transcription	Aorta	Aorta
29	chr19:23540000-23545600	Weak transcription	Lung	lung
30	chr19:23540000-23546800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr19:23540000-23549000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:23540200-23541400	Weak transcription	Psoas Muscle	Psoas
33	chr19:23540200-23542000	Weak transcription	Placenta	Placenta
34	chr19:23540800-23541600	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr19:23541200-23541600	ZNF genes & repeats	HSMM	muscle
36	chr19:23541200-23546000	ZNF genes & repeats	Brain Germinal Matrix	brain
37	chr19:23541200-23548400	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
38	chr19:23541200-23552400	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived

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