Variant report

Variant	rs889362
Chromosome Location	chr19:18758255-18758256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18713980..18716446-chr19:18757354..18760125,2	K562	blood:
2	chr19:18755921..18758838-chr19:18761971..18763862,2	K562	blood:
3	chr19:18757758..18761197-chr19:18765478..18769110,5	MCF-7	breast:
4	chr19:18758073..18760878-chr19:18781482..18783635,2	K562	blood:
5	chr19:18756524..18758579-chr19:18764245..18767050,2	K562	blood:

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10402536	0.96[CEU][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10403231	1.00[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10423102	0.84[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.94[ASN][1000 genomes]
rs10423271	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10423676	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10423852	0.91[ASN][1000 genomes]
rs1076234	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1076235	0.89[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11085237	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11085239	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11668617	1.00[CEU][hapmap];0.87[CHB][hapmap];0.84[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.92[TSI][hapmap];0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12052075	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12610845	0.89[ASW][hapmap];0.96[CEU][hapmap];0.87[CHB][hapmap];0.98[GIH][hapmap];0.90[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.97[TSI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12974161	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12974777	0.91[ASN][1000 genomes]
rs12976741	0.88[ASN][1000 genomes]
rs12980154	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs12983476	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1473115	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2014914	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34143665	0.91[ASN][1000 genomes]
rs34190814	0.94[ASN][1000 genomes]
rs3795026	0.96[CEU][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs4808146	0.82[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4808841	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4808842	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs71332133	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs889363	0.89[ASW][hapmap];1.00[CEU][hapmap];0.87[CHB][hapmap];0.89[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1057795	chr19:18453362-18883844	Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
2	nsv543925	chr19:18453362-18883844	Weak transcription Genic enhancers Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
3	nsv532615	chr19:18534867-18796031	Enhancers Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	71 gene(s)	inside rSNPs	diseases
4	nsv911281	chr19:18613917-18758255	Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
5	nsv911282	chr19:18624964-18928480	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
6	nsv833776	chr19:18638028-18782264	Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
7	nsv911286	chr19:18652844-18811112	Active TSS Flanking Active TSS Enhancers Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
8	nsv911289	chr19:18700047-18811112	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	esv1849639	chr19:18747006-18780799	Weak transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs889362	CRTC1	cis	cerebellum	SCAN
rs889362	UBA52	cis	lymphoblastoid	seeQTL

Chromatin state (count:106 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748400-18761600	Weak transcription	Aorta	Aorta
2	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr19:18748800-18758600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr19:18748800-18759200	Weak transcription	Fetal Lung	lung
5	chr19:18749200-18759000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:18749200-18759600	Weak transcription	Thymus	Thymus
7	chr19:18749200-18759800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr19:18749400-18758800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
11	chr19:18749400-18759200	Weak transcription	Gastric	stomach
12	chr19:18749400-18759400	Weak transcription	Fetal Intestine Large	intestine
13	chr19:18749400-18759600	Weak transcription	Liver	Liver
14	chr19:18749400-18759800	Weak transcription	Rectal Mucosa Donor 31	rectum
15	chr19:18749400-18760000	Weak transcription	Fetal Brain Female	brain
16	chr19:18749400-18762200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr19:18749400-18774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr19:18749600-18759800	Weak transcription	Primary T cells from cord blood	blood
19	chr19:18749800-18759200	Weak transcription	Pancreas	Pancrea
20	chr19:18749800-18759200	Weak transcription	Spleen	Spleen
21	chr19:18749800-18760800	Weak transcription	Dnd41	blood
22	chr19:18751200-18759600	Weak transcription	Stomach Mucosa	stomach
23	chr19:18752000-18758600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr19:18754800-18760000	Enhancers	Brain Substantia Nigra	brain
25	chr19:18755000-18759400	Enhancers	Skeletal Muscle Female	skeletal muscle
26	chr19:18755400-18759200	Enhancers	Skeletal Muscle Male	skeletal muscle
27	chr19:18755400-18760000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr19:18755600-18759200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr19:18755600-18759200	Weak transcription	Sigmoid Colon	Sigmoid Colon
30	chr19:18755600-18759400	Weak transcription	Colonic Mucosa	Colon
31	chr19:18755600-18759400	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr19:18755600-18762200	Weak transcription	NHEK	skin
33	chr19:18755800-18759200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr19:18755800-18759200	Weak transcription	Fetal Thymus	thymus
35	chr19:18755800-18759400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
36	chr19:18755800-18760000	Weak transcription	Primary T helper cells PMA-I stimulated	--
37	chr19:18755800-18764000	Enhancers	Right Ventricle	heart
38	chr19:18755800-18766600	Weak transcription	HepG2	liver
39	chr19:18756000-18758600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr19:18756000-18759200	Weak transcription	Primary B cells from cord blood	blood
41	chr19:18756000-18759200	Weak transcription	Primary B cells from peripheral blood	blood
42	chr19:18756000-18759400	Weak transcription	GM12878-XiMat	blood
43	chr19:18756000-18759600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr19:18756000-18759600	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr19:18756000-18759600	Weak transcription	Rectal Smooth Muscle	rectum
46	chr19:18756000-18759800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
47	chr19:18756000-18760200	Weak transcription	Fetal Brain Male	brain
48	chr19:18756200-18758600	Weak transcription	Left Ventricle	heart
49	chr19:18756200-18759200	Weak transcription	Esophagus	oesophagus
50	chr19:18756200-18759400	Weak transcription	Monocytes-CD14+_RO01746	blood

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