Variant report

Variant	rs12980154
Chromosome Location	chr19:18770119-18770120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:18769395..18771988-chr19:18793158..18795733,2	MCF-7	breast:
2	chr19:18769172..18772928-chr19:18776666..18781148,5	K562	blood:
3	chr19:18759439..18761865-chr19:18767134..18771094,4	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-CRTC1-1	chr19:18769451-18770215	NONHSAT062991

Variant related genes	Relation type
ENSG00000105662	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs10402536	0.85[CEU][hapmap];0.87[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs10403231	0.82[CEU][hapmap];0.96[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10423102	0.95[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10423271	0.90[ASN][1000 genomes]
rs10423676	0.82[CEU][hapmap];0.96[CHB][hapmap];0.95[JPT][hapmap];0.95[ASN][1000 genomes]
rs10423852	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1076235	0.84[CEU][hapmap]
rs11085237	0.84[CEU][hapmap];0.83[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs11085239	0.96[ASN][1000 genomes]
rs11668617	0.84[CEU][hapmap];0.95[CHB][hapmap];0.83[ASN][1000 genomes]
rs12052075	0.90[ASN][1000 genomes]
rs12610845	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12974161	0.93[ASN][1000 genomes]
rs12974777	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12976741	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12983476	0.94[ASN][1000 genomes]
rs1473115	0.96[ASN][1000 genomes]
rs2014914	0.90[ASN][1000 genomes]
rs34143665	0.96[ASN][1000 genomes]
rs34190814	0.92[ASN][1000 genomes]
rs3795026	0.80[CEU][hapmap];0.81[JPT][hapmap]
rs4808146	0.93[ASN][1000 genomes]
rs4808841	0.87[ASN][1000 genomes]
rs4808842	0.85[ASN][1000 genomes]
rs71332133	0.92[ASN][1000 genomes]
rs889362	0.84[CEU][hapmap];0.82[CHB][hapmap];0.95[JPT][hapmap];0.88[ASN][1000 genomes]
rs889363	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:10 , 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
9	esv1811733	chr19:18764320-18780799	Enhancers Weak transcription Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
10	esv1845237	chr19:18764320-18780799	Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:108 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18748600-18774400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr19:18749200-18778400	Weak transcription	H9 Cell Line	embryonic stem cell
3	chr19:18749400-18774000	Weak transcription	Primary T helper cells fromperipheralblood	blood
4	chr19:18756400-18778400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:18759400-18776200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr19:18759800-18778400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr19:18760200-18775000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr19:18760400-18774000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr19:18760400-18794800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr19:18760600-18774800	Weak transcription	Thymus	Thymus
11	chr19:18760800-18776200	Weak transcription	Liver	Liver
12	chr19:18760800-18778400	Weak transcription	Rectal Mucosa Donor 31	rectum
13	chr19:18762000-18770200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
14	chr19:18762200-18771200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:18762600-18774600	Weak transcription	Primary T cells from cord blood	blood
16	chr19:18762600-18775600	Weak transcription	Dnd41	blood
17	chr19:18762800-18770600	Weak transcription	Psoas Muscle	Psoas
18	chr19:18763000-18778400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
19	chr19:18765600-18772400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
20	chr19:18766000-18771200	Enhancers	Right Ventricle	heart
21	chr19:18766200-18771200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr19:18766400-18770400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr19:18766600-18770400	Enhancers	Fetal Muscle Leg	muscle
24	chr19:18766600-18770600	Enhancers	Skeletal Muscle Male	skeletal muscle
25	chr19:18766600-18770800	Enhancers	Left Ventricle	heart
26	chr19:18766600-18772400	Enhancers	Brain Hippocampus Middle	brain
27	chr19:18766600-18772400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr19:18766600-18774000	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr19:18766800-18770800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr19:18766800-18772000	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr19:18767200-18770200	Enhancers	Cortex derived primary cultured neurospheres	brain
32	chr19:18767200-18770600	Enhancers	Fetal Stomach	stomach
33	chr19:18767200-18771200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr19:18767200-18771200	Enhancers	Brain Anterior Caudate	brain
35	chr19:18767200-18772600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr19:18767200-18775000	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr19:18767400-18770400	Enhancers	Brain Substantia Nigra	brain
38	chr19:18767400-18770600	Weak transcription	Lung	lung
39	chr19:18767400-18773600	Weak transcription	HepG2	liver
40	chr19:18767400-18776200	Weak transcription	Pancreas	Pancrea
41	chr19:18767400-18778400	Weak transcription	Aorta	Aorta
42	chr19:18767600-18770600	Enhancers	HSMMtube	muscle
43	chr19:18767800-18770400	Enhancers	GM12878-XiMat	blood
44	chr19:18767800-18770400	Enhancers	HSMM	muscle
45	chr19:18767800-18770600	Enhancers	Muscle Satellite Cultured Cells	--
46	chr19:18767800-18771000	Enhancers	Duodenum Smooth Muscle	Duodenum
47	chr19:18767800-18772000	Enhancers	Brain Angular Gyrus	brain
48	chr19:18767800-18772000	Enhancers	Right Atrium	heart
49	chr19:18767800-18772600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr19:18767800-18774600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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