Variant report

Variant	rs889363
Chromosome Location	chr19:18761276-18761277
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18754096..18756985-chr19:18760445..18762017,2	MCF-7	breast:
2	chr19:18722195..18724097-chr19:18759518..18761356,2	K562	blood:
3	chr19:18752753..18754292-chr19:18759616..18761597,2	K562	blood:
4	chr19:18759533..18761540-chr19:18773488..18775282,2	K562	blood:
5	chr19:18759439..18761865-chr19:18767134..18771094,4	K562	blood:

Variant related genes	Relation type
ENSG00000105696	Chromatin interaction
ENSG00000167487	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10402536	0.96[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10403231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10423102	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs10423271	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10423676	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10423852	0.98[ASN][1000 genomes]
rs1076234	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1076235	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11085237	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11085239	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11668617	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.95[MEX][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12052075	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12610845	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];0.82[LWK][hapmap];0.96[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12974161	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12974777	0.98[ASN][1000 genomes]
rs12976741	0.95[ASN][1000 genomes]
rs12980154	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12983476	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1473115	0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2014914	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2238647	0.84[CHD][hapmap]
rs2283617	0.81[CHD][hapmap]
rs34143665	0.98[ASN][1000 genomes]
rs34190814	0.98[ASN][1000 genomes]
rs3795026	0.84[ASW][hapmap];0.96[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[YRI][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4808146	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4808841	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4808842	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs71332133	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7249956	0.86[CHD][hapmap]
rs8110573	0.86[CHD][hapmap]
rs889362	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:8 , 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	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
5	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
6	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
7	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
8	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs889363	CRTC1	cis	cerebellum	SCAN

Chromatin state (count:112 , 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	chr19:18749200-18768200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:18749400-18762200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr19:18749400-18774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr19:18755600-18762200	Weak transcription	NHEK	skin
8	chr19:18755800-18764000	Enhancers	Right Ventricle	heart
9	chr19:18755800-18766600	Weak transcription	HepG2	liver
10	chr19:18756400-18778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr19:18757400-18762000	Enhancers	Fetal Kidney	kidney
12	chr19:18758000-18762800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr19:18758400-18762600	Enhancers	Fetal Heart	heart
14	chr19:18758800-18762200	Weak transcription	K562	blood
15	chr19:18758800-18762800	Genic enhancers	Fetal Stomach	stomach
16	chr19:18758800-18763000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
17	chr19:18758800-18763000	Enhancers	Placenta	Placenta
18	chr19:18759000-18761600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr19:18759200-18762200	Genic enhancers	Spleen	Spleen
20	chr19:18759200-18762600	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
21	chr19:18759200-18763000	Enhancers	Fetal Thymus	thymus
22	chr19:18759400-18761400	Enhancers	ES-I3 Cell Line	embryonic stem cell
23	chr19:18759400-18761600	Genic enhancers	Fetal Intestine Small	intestine
24	chr19:18759400-18762000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
25	chr19:18759400-18762200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr19:18759400-18762600	Enhancers	HUVEC	blood vessel
27	chr19:18759400-18762800	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
28	chr19:18759400-18762800	Enhancers	Lung	lung
29	chr19:18759400-18776200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
30	chr19:18759600-18762000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
31	chr19:18759600-18762400	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr19:18759600-18763200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr19:18759800-18761400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr19:18759800-18762000	Flanking Active TSS	Adipose Nuclei	Adipose
35	chr19:18759800-18762200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr19:18759800-18762400	Weak transcription	Pancreas	Pancrea
37	chr19:18759800-18778400	Weak transcription	Pancreatic Islets	Pancreatic Islet
38	chr19:18760000-18762000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr19:18760000-18762400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:18760000-18762400	Flanking Active TSS	NHLF	lung
41	chr19:18760000-18762600	Enhancers	iPS-20b Cell Line	embryonic stem cell
42	chr19:18760000-18770000	Weak transcription	Gastric	stomach
43	chr19:18760000-18770000	Weak transcription	Stomach Mucosa	stomach
44	chr19:18760200-18762000	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr19:18760200-18762000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
46	chr19:18760200-18762200	Flanking Active TSS	Rectal Smooth Muscle	rectum
47	chr19:18760200-18762400	Flanking Active TSS	Stomach Smooth Muscle	stomach
48	chr19:18760200-18762600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr19:18760200-18775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr19:18760400-18761400	Enhancers	Brain Substantia Nigra	brain

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