Variant report

Variant	rs62112569
Chromosome Location	chr19:36828766-36828767
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs12461529	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12462725	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17206379	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2271842	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2385802	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2857	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2945955	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945956	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2945989	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2967508	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967511	0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2967519	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3098393	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3111555	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3111556	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810326	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56378871	0.88[ASN][1000 genomes]
rs61706074	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112567	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112568	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112624	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62112631	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62112632	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62113869	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7248731	0.82[AFR][1000 genomes]
rs7253122	0.87[ASN][1000 genomes]
rs73043845	0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73043902	0.88[ASN][1000 genomes]
rs8104241	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1063208	chr19:36743461-36847486	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	6 gene(s)	inside rSNPs	diseases
2	nsv1056901	chr19:36749658-36847486	Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription Enhancers Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1061054	chr19:36751703-36847486	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
4	nsv1055260	chr19:36752221-36847486	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
5	nsv1056850	chr19:36752663-36847486	Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv1064983	chr19:36752663-36847625	Weak transcription Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
7	nsv1057579	chr19:36752663-36847822	Strong transcription Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
8	esv1825146	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Flanking Active TSS Strong transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
9	esv1837043	chr19:36800927-36846993	ZNF genes & repeats Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island lncRNA	6 gene(s)	inside rSNPs	diseases
10	nsv2474	chr19:36804469-36865415	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
11	esv2763143	chr19:36805705-36847498	Strong transcription Active TSS Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
12	nsv1059568	chr19:36806475-36847864	Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
13	esv1823621	chr19:36807288-36845863	Weak transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Genic enhancers Bivalent/Poised TSS	TF binding region CpG island lncRNA	3 gene(s)	inside rSNPs	diseases
14	nsv1064343	chr19:36807288-36853102	Weak transcription Strong transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
15	nsv833816	chr19:36824257-37034287	ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs62112569	LINC00665	cis	Skin Sun Exposed Lower leg	GTEx
rs62112569	LINC00665	cis	Nerve Tibial	GTEx
rs62112569	LINC00665	cis	Thyroid	GTEx
rs62112569	CTD-3162L10.1	cis	Muscle Skeletal	GTEx
rs62112569	CTD-3162L10.1	cis	Nerve Tibial	GTEx
rs62112569	LINC00665	cis	Muscle Skeletal	GTEx
rs62112569	ZNF545	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:36823200-36830200	Weak transcription	Fetal Brain Male	brain
2	chr19:36823400-36829000	Weak transcription	Placenta	Placenta
3	chr19:36823400-36829200	Weak transcription	Fetal Muscle Leg	muscle
4	chr19:36823400-36830200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr19:36823400-36830200	Weak transcription	Brain Angular Gyrus	brain
6	chr19:36823400-36830200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr19:36823400-36830200	Weak transcription	Brain Substantia Nigra	brain
8	chr19:36823400-36830200	Weak transcription	Colon Smooth Muscle	Colon
9	chr19:36823400-36830400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:36823600-36830000	Weak transcription	Brain Anterior Caudate	brain
11	chr19:36823600-36830000	Weak transcription	Brain Germinal Matrix	brain
12	chr19:36823600-36830200	Weak transcription	H9 Cell Line	embryonic stem cell
13	chr19:36823600-36830200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr19:36823600-36830200	Weak transcription	Fetal Brain Female	brain
15	chr19:36823600-36830200	Weak transcription	Ovary	ovary
16	chr19:36823600-36831400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
17	chr19:36823800-36853600	ZNF genes & repeats	Liver	Liver
18	chr19:36824600-36838000	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr19:36825000-36830200	Weak transcription	Rectal Smooth Muscle	rectum
20	chr19:36825000-36836600	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr19:36826600-36840000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
22	chr19:36827000-36831800	Weak transcription	Fetal Stomach	stomach
23	chr19:36827200-36828800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr19:36827200-36828800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr19:36827200-36828800	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum
26	chr19:36827200-36839800	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr19:36827200-36840000	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
28	chr19:36827200-36841600	ZNF genes & repeats	Primary hematopoietic stem cells	blood
29	chr19:36827200-36844200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr19:36827200-36862200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr19:36827400-36828800	ZNF genes & repeats	Duodenum Mucosa	Duodenum
32	chr19:36827400-36828800	Strong transcription	Dnd41	blood
33	chr19:36827400-36830000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
34	chr19:36827400-36833800	ZNF genes & repeats	iPS-20b Cell Line	embryonic stem cell
35	chr19:36827400-36836800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
36	chr19:36827400-36839800	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
37	chr19:36827400-36840000	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
38	chr19:36827400-36843400	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
39	chr19:36827600-36828800	Strong transcription	Brain Inferior Temporal Lobe	brain
40	chr19:36827600-36832400	ZNF genes & repeats	Primary B cells from cord blood	blood
41	chr19:36827800-36829800	Weak transcription	Brain Hippocampus Middle	brain
42	chr19:36827800-36830200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr19:36828000-36829400	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr19:36828200-36829400	Weak transcription	HUES64 Cell Line	embryonic stem cell
45	chr19:36828200-36829800	Weak transcription	Stomach Smooth Muscle	stomach
46	chr19:36828400-36828800	ZNF genes & repeats	Primary T helper 17 cells PMA-I stimulated	--
47	chr19:36828400-36832600	ZNF genes & repeats	A549	lung
48	chr19:36828600-36828800	ZNF genes & repeats	Fetal Heart	heart
49	chr19:36828600-36830000	Weak transcription	Fetal Kidney	kidney
50	chr19:36828600-36830200	Weak transcription	Left Ventricle	heart

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