Variant report

Variant	rs4806414
Chromosome Location	chr19:37638788-37638789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-ZNF585A-2	chr19:37638507-37641036	NONHSAT066071

Extended variants
information (count: 77 )
Associated
traits (count: 12 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10401380	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10401525	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10401561	0.87[EUR][1000 genomes]
rs10402050	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10404069	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10404973	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10405372	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10406612	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[EUR][1000 genomes]
rs10407014	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10407224	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10407265	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10408199	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10410905	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10411037	0.88[EUR][1000 genomes]
rs10411176	0.84[CEU][hapmap];1.00[CHB][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.82[YRI][hapmap];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10412236	0.86[EUR][1000 genomes]
rs10413101	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10413304	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10414107	0.87[EUR][1000 genomes]
rs10414227	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10414983	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10417545	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10418314	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10419174	0.92[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10419845	0.81[EUR][1000 genomes]
rs10422428	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10424841	0.85[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.94[TSI][hapmap];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10425441	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10426093	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11084873	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12972146	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975706	0.84[EUR][1000 genomes]
rs12978093	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12983153	0.88[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13346284	0.87[EUR][1000 genomes]
rs1617883	0.88[EUR][1000 genomes]
rs1624293	0.89[CEU][hapmap]
rs1628959	0.83[EUR][1000 genomes]
rs1644702	0.84[EUR][1000 genomes]
rs1644704	0.84[EUR][1000 genomes]
rs2385412	0.87[EUR][1000 genomes]
rs28462002	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28631881	0.85[EUR][1000 genomes]
rs28660259	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28701616	0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34193103	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs34915391	0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35522655	0.87[EUR][1000 genomes]
rs35655645	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4473303	0.82[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4805198	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4805207	0.84[CEU][hapmap];0.88[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.86[MKK][hapmap];0.88[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4805208	0.84[CEU][hapmap];1.00[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.88[TSI][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4806406	0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62108899	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs62109879	0.88[EUR][1000 genomes]
rs7246473	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7247758	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7249696	0.81[ASN][1000 genomes]
rs7259878	0.87[EUR][1000 genomes]
rs8101338	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8111936	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8112011	0.82[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064851	chr19:36910259-37689721	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	62 gene(s)	inside rSNPs	diseases
2	nsv1065698	chr19:36916796-37690124	Active TSS ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	nsv543999	chr19:36916796-37690124	Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Strong transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv529817	chr19:36930549-37654062	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
5	nsv918028	chr19:37020645-38014526	Weak transcription ZNF genes & repeats Active TSS Enhancers Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
6	esv3507199	chr19:37284708-37805639	Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Active TSS 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 miRNA target site	27 gene(s)	inside rSNPs	diseases
7	esv3507200	chr19:37284708-37805639	ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
8	esv3497360	chr19:37290273-37745365	ZNF genes & repeats Active TSS Flanking Active TSS Weak transcription Strong transcription Enhancers Genic enhancers 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	25 gene(s)	inside rSNPs	diseases
9	esv3497361	chr19:37290273-37745365	Active TSS ZNF genes & repeats Strong transcription Weak 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 Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
10	nsv458568	chr19:37325826-37747108	Strong transcription ZNF genes & repeats Genic enhancers Active TSS Weak transcription Enhancers Flanking Active TSS 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	22 gene(s)	inside rSNPs	diseases
11	nsv579461	chr19:37325826-37747108	Strong transcription Weak transcription Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
12	nsv911652	chr19:37437106-37774299	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv911654	chr19:37487632-37758082	Strong transcription Active TSS ZNF genes & repeats Weak transcription Flanking Active TSS Enhancers Genic enhancers 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	16 gene(s)	inside rSNPs	diseases
14	nsv2477	chr19:37617348-37662207	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:12)

SNP	Gene	Cis/trans	Tissue	Source
rs4806414	PAFAH1B3	cis	cerebellum	SCAN
rs4806414	ZNF420	cis	lymphoblastoid	seeQTL
rs4806414	MEGF8	cis	cerebellum	SCAN
rs4806414	AXL	cis	cerebellum	SCAN
rs4806414	XRCC1	cis	parietal	SCAN
rs4806414	SNRPD2	cis	parietal	SCAN
rs4806414	SERTAD3	cis	parietal	SCAN
rs4806414	CYP2B6	cis	cerebellum	SCAN
rs4806414	CEACAM16	cis	cerebellum	SCAN
rs4806414	VASP	cis	parietal	SCAN
rs4806414	EXOSC5	cis	cerebellum	SCAN
rs4806414	ITPKC	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:37613400-37642200	ZNF genes & repeats	Adipose Nuclei	Adipose
2	chr19:37613400-37642200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
3	chr19:37613800-37662200	ZNF genes & repeats	Liver	Liver
4	chr19:37634400-37657800	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr19:37634800-37642600	ZNF genes & repeats	Brain Germinal Matrix	brain
6	chr19:37635000-37641800	ZNF genes & repeats	Skeletal Muscle Female	skeletal muscle
7	chr19:37635000-37642000	ZNF genes & repeats	Fetal Brain Male	brain
8	chr19:37635000-37642200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr19:37635000-37656200	ZNF genes & repeats	Fetal Brain Female	brain
10	chr19:37635200-37642200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
11	chr19:37635200-37642200	ZNF genes & repeats	Cortex derived primary cultured neurospheres	brain
12	chr19:37635200-37642200	ZNF genes & repeats	Fetal Lung	lung
13	chr19:37635200-37642200	ZNF genes & repeats	Ovary	ovary
14	chr19:37635200-37661400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
15	chr19:37635200-37661600	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr19:37635400-37642000	ZNF genes & repeats	Duodenum Mucosa	Duodenum
17	chr19:37635400-37642200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
18	chr19:37635600-37642200	ZNF genes & repeats	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr19:37635600-37642200	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
20	chr19:37635800-37642000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
21	chr19:37635800-37642200	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
22	chr19:37635800-37642800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr19:37636200-37642000	ZNF genes & repeats	Psoas Muscle	Psoas
24	chr19:37636600-37639200	Weak transcription	Fetal Heart	heart
25	chr19:37637400-37639000	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
26	chr19:37637400-37642000	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr19:37637400-37642000	ZNF genes & repeats	Brain Angular Gyrus	brain
28	chr19:37637400-37642200	ZNF genes & repeats	HUES48 Cell Line	embryonic stem cell
29	chr19:37637400-37642200	ZNF genes & repeats	Brain Hippocampus Middle	brain
30	chr19:37637400-37642200	ZNF genes & repeats	Brain Inferior Temporal Lobe	brain
31	chr19:37637400-37642200	ZNF genes & repeats	Dnd41	blood
32	chr19:37637400-37656800	ZNF genes & repeats	Brain Anterior Caudate	brain
33	chr19:37637600-37640600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:37637600-37642200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
35	chr19:37637600-37642400	ZNF genes & repeats	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
36	chr19:37637800-37641800	ZNF genes & repeats	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr19:37637800-37642000	ZNF genes & repeats	Primary T cells from cord blood	blood
38	chr19:37638000-37639800	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr19:37638200-37639000	Weak transcription	Left Ventricle	heart
40	chr19:37638200-37640200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
41	chr19:37638200-37640400	Weak transcription	Gastric	stomach
42	chr19:37638200-37640400	Weak transcription	Thymus	Thymus
43	chr19:37638400-37640400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
44	chr19:37638400-37640400	Weak transcription	Placenta	Placenta
45	chr19:37638400-37640400	Weak transcription	Lung	lung
46	chr19:37638400-37640400	Weak transcription	Pancreas	Pancrea

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