Variant report

Variant	rs12980289
Chromosome Location	chr19:40320339-40320340
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:40318662..40321360-chr19:40322185..40325984,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105204	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs10422280	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11880094	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11880956	0.96[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.84[YRI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11883249	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12975624	0.86[CHB][hapmap];0.86[GIH][hapmap];0.86[MEX][hapmap]
rs12986299	0.84[CHB][hapmap]
rs2072290	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.90[MKK][hapmap];1.00[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2354800	1.00[CEU][hapmap];0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810383	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3810386	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4803297	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs616650	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.98[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs619350	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62106867	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6508912	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6508913	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs718066	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7246501	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7248926	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7253739	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7254914	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7258351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3329492	chr19:40198535-40437035	Active TSS Flanking Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
2	esv2758498	chr19:40227904-40521130	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
3	esv2758760	chr19:40227904-40521130	Genic enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
4	nsv428022	chr19:40227904-40521130	Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
5	nsv911696	chr19:40310497-40344648	Active TSS Strong transcription Weak transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
6	nsv9725	chr19:40315519-40412523	Flanking Active TSS Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region miRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12980289	PHLDB3	cis	parietal	SCAN
rs12980289	B9D2	cis	cerebellum	SCAN
rs12980289	ERF	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:40312000-40323200	Strong transcription	A549	lung
2	chr19:40315200-40320400	Weak transcription	Aorta	Aorta
3	chr19:40315200-40320400	Weak transcription	Psoas Muscle	Psoas
4	chr19:40315400-40322800	Strong transcription	Placenta	Placenta
5	chr19:40315800-40320400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr19:40315800-40320400	Strong transcription	NHLF	lung
7	chr19:40315800-40322200	Strong transcription	Placenta Amnion	Placenta Amnion
8	chr19:40315800-40322400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:40315800-40322400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr19:40315800-40322600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr19:40315800-40323400	Weak transcription	Right Atrium	heart
12	chr19:40315800-40323600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr19:40316000-40320600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr19:40316000-40320600	Weak transcription	HMEC	breast
15	chr19:40316000-40321000	Strong transcription	Colonic Mucosa	Colon
16	chr19:40316000-40321200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
17	chr19:40316000-40321800	Genic enhancers	Skeletal Muscle Female	skeletal muscle
18	chr19:40316000-40321800	Strong transcription	Thymus	Thymus
19	chr19:40316000-40322000	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr19:40316000-40322000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr19:40316000-40322200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr19:40316000-40322400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
23	chr19:40316000-40322400	Strong transcription	Brain Inferior Temporal Lobe	brain
24	chr19:40316000-40322400	Strong transcription	Lung	lung
25	chr19:40316000-40322600	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr19:40316000-40322800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr19:40316000-40322800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
28	chr19:40316000-40322800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
29	chr19:40316000-40323000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr19:40316000-40323200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr19:40316000-40323200	Strong transcription	NHEK	skin
32	chr19:40316200-40320400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
33	chr19:40316200-40320600	Strong transcription	Spleen	Spleen
34	chr19:40316200-40321400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
35	chr19:40316200-40321600	Weak transcription	Fetal Brain Male	brain
36	chr19:40316200-40321600	Strong transcription	Right Ventricle	heart
37	chr19:40316200-40321800	Strong transcription	Primary neutrophils fromperipheralblood	blood
38	chr19:40316200-40321800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
39	chr19:40316200-40322000	Strong transcription	H1 Cell Line	embryonic stem cell
40	chr19:40316200-40322000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr19:40316200-40322200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
42	chr19:40316200-40322200	Strong transcription	Adipose Nuclei	Adipose
43	chr19:40316200-40322400	Strong transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr19:40316200-40322400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr19:40316200-40322400	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
46	chr19:40316200-40322400	Strong transcription	Duodenum Smooth Muscle	Duodenum
47	chr19:40316200-40322400	Strong transcription	Fetal Brain Female	brain
48	chr19:40316200-40322600	Strong transcription	Cortex derived primary cultured neurospheres	brain
49	chr19:40316200-40322600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
50	chr19:40316200-40322600	Strong transcription	Brain Cingulate Gyrus	brain

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