Variant report

Variant	rs612578
Chromosome Location	chr19:20843876-20843877
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 65 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:46)

rs_ID	r²[population]
rs11085372	0.84[ASN][1000 genomes]
rs11085373	0.84[ASN][1000 genomes]
rs11671682	0.81[AMR][1000 genomes]
rs11879869	0.84[ASN][1000 genomes]
rs11879894	0.84[ASN][1000 genomes]
rs11882762	0.84[ASN][1000 genomes]
rs12460938	0.84[ASN][1000 genomes]
rs12460942	0.84[ASN][1000 genomes]
rs12460958	0.84[ASN][1000 genomes]
rs12461005	0.84[ASN][1000 genomes]
rs12461026	0.84[ASN][1000 genomes]
rs12971404	0.82[ASN][1000 genomes]
rs12971592	0.84[ASN][1000 genomes]
rs12980835	0.84[ASN][1000 genomes]
rs12981003	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12981246	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12981702	0.80[ASN][1000 genomes]
rs12985845	0.84[ASN][1000 genomes]
rs2081890	0.84[ASN][1000 genomes]
rs2336612	0.84[ASN][1000 genomes]
rs2336613	0.84[ASN][1000 genomes]
rs2336614	0.84[ASN][1000 genomes]
rs274797	0.88[ASN][1000 genomes]
rs2878754	0.84[ASN][1000 genomes]
rs2878755	0.84[ASN][1000 genomes]
rs35076092	0.84[ASN][1000 genomes]
rs35191658	0.84[ASN][1000 genomes]
rs4393699	0.84[ASN][1000 genomes]
rs4442934	0.84[ASN][1000 genomes]
rs4574049	0.84[ASN][1000 genomes]
rs4809091	0.84[ASN][1000 genomes]
rs4809093	0.84[ASN][1000 genomes]
rs556901	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs561483	0.82[ASN][1000 genomes]
rs561663	0.84[ASN][1000 genomes]
rs561718	0.84[ASN][1000 genomes]
rs561724	0.84[ASN][1000 genomes]
rs594210	0.84[ASN][1000 genomes]
rs613462	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs656864	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs659147	0.87[ASN][1000 genomes]
rs672887	0.86[ASN][1000 genomes]
rs7248221	0.84[ASN][1000 genomes]
rs74182981	0.81[AMR][1000 genomes]
rs8100460	0.84[ASN][1000 genomes]
rs8101051	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:19 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv911325	chr19:20151257-21071548	ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	49 gene(s)	inside rSNPs	diseases
2	esv2758489	chr19:20574295-20845947	Strong transcription Active TSS ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
3	esv2758749	chr19:20574295-20845947	ZNF genes & repeats Genic enhancers Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	13 gene(s)	inside rSNPs	diseases
4	nsv530804	chr19:20574295-21001349	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	21 gene(s)	inside rSNPs	diseases
5	nsv978786	chr19:20818886-20884983	Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv911407	chr19:20818886-20885811	ZNF genes & repeats Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv911408	chr19:20818886-20885811	Enhancers Genic enhancers ZNF genes & repeats Strong transcription Weak transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv1065039	chr19:20818886-20977326	Active TSS Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
9	esv2751781	chr19:20818886-20985425	ZNF genes & repeats Enhancers Weak transcription Strong transcription Active TSS Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
10	nsv578921	chr19:20818886-20985425	ZNF genes & repeats Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
11	nsv458510	chr19:20818886-20987550	Flanking Active TSS ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
12	nsv578910	chr19:20818886-20987550	Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Active TSS Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
13	nsv578917	chr19:20818886-20989873	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription 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	10 gene(s)	inside rSNPs	diseases
14	nsv578918	chr19:20818886-21008212	ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	esv3447275	chr19:20818886-21030779	Strong transcription Weak transcription ZNF genes & repeats 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	13 gene(s)	inside rSNPs	diseases
16	esv2752729	chr19:20818886-21169554	ZNF genes & repeats Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
17	nsv1062776	chr19:20818886-21273361	Weak transcription Active TSS Enhancers ZNF genes & repeats Strong transcription Flanking 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	32 gene(s)	inside rSNPs	diseases
18	nsv932110	chr19:20818886-21278952	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS 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	32 gene(s)	inside rSNPs	diseases
19	esv2763043	chr19:20818886-21290543	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs612578	ZNF738	cis	parietal	SCAN
rs612578	ZNF626	cis	parietal	SCAN
rs612578	SLC27A1	cis	parietal	SCAN

Chromatin state (count:124 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:20840000-20844400	ZNF genes & repeats	Fetal Brain Male	brain
2	chr19:20841000-20844600	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
3	chr19:20842000-20844400	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr19:20842200-20844600	Active TSS	Colonic Mucosa	Colon
5	chr19:20842400-20844600	Active TSS	HUES48 Cell Line	embryonic stem cell
6	chr19:20842400-20844600	Active TSS	K562	blood
7	chr19:20842400-20844800	Active TSS	Fetal Kidney	kidney
8	chr19:20842600-20844200	Active TSS	HUES6 Cell Line	embryonic stem cell
9	chr19:20842600-20844400	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr19:20842600-20844400	Active TSS	H9 Cell Line	embryonic stem cell
11	chr19:20842600-20844800	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr19:20842600-20844800	Active TSS	Primary T cells from cord blood	blood
13	chr19:20842800-20844400	ZNF genes & repeats	iPS-18 Cell Line	embryonic stem cell
14	chr19:20842800-20844600	Active TSS	ES-I3 Cell Line	embryonic stem cell
15	chr19:20842800-20844600	Active TSS	Duodenum Mucosa	Duodenum
16	chr19:20842800-20844600	Active TSS	Rectal Smooth Muscle	rectum
17	chr19:20842800-20844600	Active TSS	HSMMtube	muscle
18	chr19:20842800-20844600	Active TSS	Osteobl	bone
19	chr19:20842800-20845200	Active TSS	HepG2	liver
20	chr19:20843000-20844400	Active TSS	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:20843000-20844400	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr19:20843000-20844600	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
23	chr19:20843000-20844600	Active TSS	iPS-20b Cell Line	embryonic stem cell
24	chr19:20843000-20844600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
25	chr19:20843000-20844600	Active TSS	Placenta	Placenta
26	chr19:20843000-20844600	Active TSS	Ovary	ovary
27	chr19:20843000-20844600	Active TSS	Rectal Mucosa Donor 29	rectum
28	chr19:20843000-20844600	Active TSS	Rectal Mucosa Donor 31	rectum
29	chr19:20843000-20844600	Active TSS	NH-A	brain
30	chr19:20843000-20844800	Active TSS	Duodenum Smooth Muscle	Duodenum
31	chr19:20843200-20844000	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr19:20843200-20844200	Active TSS	ES-WA7 Cell Line	embryonic stem cell
33	chr19:20843200-20844200	Active TSS	Fetal Heart	heart
34	chr19:20843200-20844400	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
35	chr19:20843200-20844400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
36	chr19:20843200-20844400	Active TSS	Aorta	Aorta
37	chr19:20843200-20844400	Active TSS	Pancreatic Islets	Pancreatic Islet
38	chr19:20843200-20844400	Active TSS	Gastric	stomach
39	chr19:20843200-20844400	Active TSS	Pancreas	Pancrea
40	chr19:20843200-20844600	Active TSS	Primary T helper naive cells fromperipheralblood	blood
41	chr19:20843200-20844600	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr19:20843200-20844600	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr19:20843200-20844600	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr19:20843200-20844600	Active TSS	Colon Smooth Muscle	Colon
45	chr19:20843200-20844600	Active TSS	Fetal Brain Female	brain
46	chr19:20843200-20844600	Active TSS	Stomach Smooth Muscle	stomach
47	chr19:20843200-20844600	Active TSS	HMEC	breast
48	chr19:20843200-20844600	Active TSS	HSMM	muscle
49	chr19:20843200-20844600	Active TSS	NHDF-Ad	bronchial
50	chr19:20843200-20844600	Active TSS	NHLF	lung

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