Variant report

Variant	rs3867193
Chromosome Location	chr19:21009030-21009031
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11881061	0.81[ASN][1000 genomes]
rs11881723	0.86[ASN][1000 genomes]
rs11882542	0.83[ASN][1000 genomes]
rs11882548	0.83[ASN][1000 genomes]
rs12150898	0.96[ASN][1000 genomes]
rs1465429	0.84[ASN][1000 genomes]
rs16997288	0.83[ASN][1000 genomes]
rs16997290	0.87[ASN][1000 genomes]
rs1985456	0.82[ASN][1000 genomes]
rs389515	0.83[ASN][1000 genomes]
rs55965424	0.82[ASN][1000 genomes]
rs56142010	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57163436	0.81[ASN][1000 genomes]
rs58780581	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs59782053	0.81[ASN][1000 genomes]
rs59841381	0.82[ASN][1000 genomes]
rs59964227	0.89[ASN][1000 genomes]
rs59977060	0.85[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60969663	0.89[ASN][1000 genomes]
rs61385453	0.82[ASN][1000 genomes]
rs61467776	0.82[ASN][1000 genomes]
rs61520244	0.83[ASN][1000 genomes]
rs62123184	0.84[ASN][1000 genomes]
rs62123185	0.84[ASN][1000 genomes]
rs62123201	0.84[ASN][1000 genomes]
rs62123213	0.84[ASN][1000 genomes]
rs62123220	0.84[ASN][1000 genomes]
rs62123227	0.81[ASN][1000 genomes]
rs62123229	0.84[ASN][1000 genomes]
rs62123230	0.84[ASN][1000 genomes]
rs62124028	0.82[ASN][1000 genomes]
rs62124029	0.82[ASN][1000 genomes]
rs62124032	0.82[ASN][1000 genomes]
rs62125572	0.81[ASN][1000 genomes]
rs62125619	0.81[ASN][1000 genomes]
rs62125623	0.82[ASN][1000 genomes]
rs62125648	0.86[ASN][1000 genomes]
rs62125651	0.96[ASN][1000 genomes]
rs73530516	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:21 , 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	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
3	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
4	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
5	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
6	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
7	esv3338155	chr19:20845947-21015656	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
8	esv3319109	chr19:20845947-21015695	Strong transcription ZNF genes & repeats Active TSS Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
9	esv3319110	chr19:20845947-21015695	Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Strong transcription Weak transcription 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	11 gene(s)	inside rSNPs	diseases
10	nsv1056154	chr19:20845947-21021053	Enhancers ZNF genes & repeats Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
11	nsv543940	chr19:20845947-21021053	Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
12	nsv1067170	chr19:20845947-21041038	Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv458512	chr19:20845947-21041350	Enhancers ZNF genes & repeats Active TSS Strong transcription Weak transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
14	nsv578926	chr19:20845947-21041350	Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
15	nsv578935	chr19:20845947-21048883	Strong transcription ZNF genes & repeats Active TSS Weak transcription Flanking Active TSS 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	12 gene(s)	inside rSNPs	diseases
16	nsv578936	chr19:20845947-21049204	Weak transcription ZNF genes & repeats Strong transcription Active TSS Transcr. at gene 5' and 3' Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
17	nsv1064103	chr19:20845947-21062996	ZNF genes & repeats Active TSS Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
18	nsv578942	chr19:20899284-21049204	ZNF genes & repeats Active TSS Weak transcription Strong transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
19	nsv578944	chr19:20946275-21048883	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
20	nsv578945	chr19:20980958-21041350	Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Enhancers	TF binding region lncRNA	4 gene(s)	inside rSNPs	diseases
21	nsv1063954	chr19:21000562-21177577	Weak transcription ZNF genes & repeats Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs3867193	USHBP1	cis	cerebellum	SCAN
rs3867193	SUGP1	cis	parietal	SCAN
rs3867193	ZNF85	Cis_1M	lymphoblastoid	RTeQTL
rs3867193	ZNF682	cis	cerebellum	SCAN

Chromatin state (count:27 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:21006800-21009200	ZNF genes & repeats	H1 Cell Line	embryonic stem cell
2	chr19:21006800-21009200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:21006800-21009200	ZNF genes & repeats	Primary B cells from cord blood	blood
4	chr19:21006800-21009200	ZNF genes & repeats	Ovary	ovary
5	chr19:21006800-21009200	ZNF genes & repeats	Dnd41	blood
6	chr19:21006800-21009400	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr19:21006800-21009600	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
8	chr19:21006800-21011200	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr19:21007000-21009200	ZNF genes & repeats	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr19:21007000-21009200	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
11	chr19:21007000-21009200	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
12	chr19:21007000-21009200	ZNF genes & repeats	Primary T helper cells PMA-I stimulated	--
13	chr19:21007000-21009400	ZNF genes & repeats	Monocytes-CD14+_RO01746	blood
14	chr19:21007200-21009200	ZNF genes & repeats	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr19:21007200-21009200	ZNF genes & repeats	Duodenum Smooth Muscle	Duodenum
16	chr19:21007200-21009400	ZNF genes & repeats	Primary T cells from cord blood	blood
17	chr19:21007200-21009400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
18	chr19:21007400-21009200	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
19	chr19:21007800-21009200	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
20	chr19:21008200-21009200	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr19:21008400-21009200	ZNF genes & repeats	Liver	Liver
22	chr19:21008400-21009400	ZNF genes & repeats	Adipose Nuclei	Adipose
23	chr19:21008800-21009200	ZNF genes & repeats	Aorta	Aorta
24	chr19:21008800-21009200	ZNF genes & repeats	Duodenum Mucosa	Duodenum
25	chr19:21008800-21009200	ZNF genes & repeats	Left Ventricle	heart
26	chr19:21008800-21009200	ZNF genes & repeats	Pancreas	Pancrea
27	chr19:21008800-21009200	ZNF genes & repeats	Rectal Mucosa Donor 31	rectum

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