Variant report

Variant	rs68016680
Chromosome Location	chr19:21769749-21769750
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF100-2	chr19:21769665-21770045	ENSG00000249473
2	lnc-ZNF100-2	chr19:21769665-21770179	NONHSAT063726
3	lnc-ZNF100-2	chr19:21769665-21770124	ENSG00000268555.1

Extended variants
information (count: 40 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10406824	0.94[ASN][1000 genomes]
rs10406870	0.94[ASN][1000 genomes]
rs12974019	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12982768	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1520073	0.94[ASN][1000 genomes]
rs1533675	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1533676	0.85[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2562399	0.94[ASN][1000 genomes]
rs2562473	0.94[ASN][1000 genomes]
rs2681380	0.94[ASN][1000 genomes]
rs2681382	0.94[ASN][1000 genomes]
rs2681383	0.94[ASN][1000 genomes]
rs2681384	0.94[ASN][1000 genomes]
rs34332442	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35506714	0.94[ASN][1000 genomes]
rs35595475	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35991360	0.94[ASN][1000 genomes]
rs4574048	0.94[ASN][1000 genomes]
rs56764276	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs62108335	0.88[ASN][1000 genomes]
rs62110212	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7251810	0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7257322	0.91[ASN][1000 genomes]
rs74167858	0.94[ASN][1000 genomes]
rs74167860	0.80[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8103967	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8113074	0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs880896	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs939301	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3414204	chr19:21301761-21839451	ZNF genes & repeats Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	esv3325271	chr19:21445407-21792817	Weak transcription ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Genic enhancers Enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
3	nsv578952	chr19:21535707-21868584	Genic enhancers Active TSS ZNF genes & repeats Enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
4	nsv833782	chr19:21663537-21845722	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
5	nsv1059328	chr19:21691123-21775948	Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1056332	chr19:21746555-21807647	ZNF genes & repeats Active TSS Enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	nsv828505	chr19:21749342-21770133	ZNF genes & repeats Active TSS Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
8	nsv543947	chr19:21749857-21772586	Enhancers Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Weak transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	n/a
9	nsv911422	chr19:21752009-21973929	ZNF genes & repeats Strong transcription Active TSS Genic enhancers Weak transcription Flanking Active TSS 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	13 gene(s)	inside rSNPs	diseases
10	nsv543948	chr19:21763457-21775948	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	n/a
11	nsv960938	chr19:21766627-21785276	Active TSS Weak transcription Enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs68016680	RP11-678G14.3	cis	Whole Blood	GTEx
rs68016680	ZNF429	cis	Whole Blood	GTEx

Chromatin state (count:97 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21766200-21770600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
2	chr19:21767600-21770800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
3	chr19:21767800-21770800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr19:21767800-21771000	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr19:21768000-21770000	Bivalent/Poised TSS	Brain Anterior Caudate	brain
6	chr19:21768000-21770000	ZNF genes & repeats	Esophagus	oesophagus
7	chr19:21768000-21770000	Active TSS	Rectal Mucosa Donor 31	rectum
8	chr19:21768000-21770600	Active TSS	Rectal Smooth Muscle	rectum
9	chr19:21768200-21770600	Active TSS	Fetal Intestine Large	intestine
10	chr19:21768400-21770200	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
11	chr19:21768400-21770200	Bivalent/Poised TSS	Fetal Stomach	stomach
12	chr19:21768400-21770600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr19:21768600-21770400	Active TSS	Pancreas	Pancrea
14	chr19:21768600-21770600	Active TSS	Fetal Intestine Small	intestine
15	chr19:21769000-21769800	Flanking Bivalent TSS/Enh	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr19:21769000-21769800	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr19:21769000-21769800	Active TSS	Primary T helper naive cells from peripheral blood	blood
18	chr19:21769000-21769800	Active TSS	Aorta	Aorta
19	chr19:21769000-21769800	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:21769000-21769800	Active TSS	Brain Substantia Nigra	brain
21	chr19:21769000-21769800	Active TSS	HSMMtube	muscle
22	chr19:21769000-21770000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
23	chr19:21769000-21770000	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr19:21769000-21770000	Bivalent/Poised TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
25	chr19:21769000-21770000	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
26	chr19:21769000-21770000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
27	chr19:21769000-21770000	Bivalent/Poised TSS	Primary neutrophils fromperipheralblood	blood
28	chr19:21769000-21770000	Bivalent Enhancer	Primary B cells from peripheral blood	blood
29	chr19:21769000-21770000	Active TSS	Primary T cells from cord blood	blood
30	chr19:21769000-21770000	Active TSS	Primary T helper cells PMA-I stimulated	--
31	chr19:21769000-21770000	Active TSS	Primary T helper cells fromperipheralblood	blood
32	chr19:21769000-21770000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
33	chr19:21769000-21770000	Bivalent/Poised TSS	Brain Angular Gyrus	brain
34	chr19:21769000-21770000	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
35	chr19:21769000-21770000	Active TSS	Gastric	stomach
36	chr19:21769000-21770000	Active TSS	Ovary	ovary
37	chr19:21769000-21770000	Active TSS	Rectal Mucosa Donor 29	rectum
38	chr19:21769000-21770000	Active TSS	Osteobl	bone
39	chr19:21769000-21770200	Active TSS	iPS-15b Cell Line	embryonic stem cell
40	chr19:21769000-21770200	Active TSS	Breast Myoepithelial Primary Cells	Breast
41	chr19:21769000-21770200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
42	chr19:21769000-21770200	Active TSS	Primary T killer naive cells fromperipheralblood	blood
43	chr19:21769000-21770200	Flanking Active TSS	Adipose Nuclei	Adipose
44	chr19:21769000-21770200	Flanking Active TSS	Brain Hippocampus Middle	brain
45	chr19:21769000-21770200	Active TSS	Fetal Kidney	kidney
46	chr19:21769000-21770200	Active TSS	Psoas Muscle	Psoas
47	chr19:21769000-21770200	Active TSS	Right Atrium	heart
48	chr19:21769000-21770200	Flanking Bivalent TSS/Enh	Monocytes-CD14+_RO01746	blood
49	chr19:21769000-21770600	ZNF genes & repeats	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr19:21769200-21769800	Bivalent/Poised TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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