Variant report

Variant	rs833915
Chromosome Location	chr19:38474060-38474061
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38472838..38474664-chr19:38494090..38496793,2	MCF-7	breast:
2	chr19:38472927..38474902-chr19:38482178..38484229,2	K562	blood:
3	chr19:38470130..38474074-chr19:38479565..38484723,5	MCF-7	breast:
4	chr19:38473416..38476574-chr19:38478709..38480543,3	MCF-7	breast:
5	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:

Extended variants
information (count: 30 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs10422056	1.00[CHB][hapmap]
rs11083439	1.00[CHB][hapmap]
rs1632177	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1643464	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1643465	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1643470	1.00[ASW][hapmap];0.80[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1643472	0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1725468	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1725486	0.90[ASN][1000 genomes]
rs1725490	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs241937	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs241940	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs241941	1.00[CHB][hapmap]
rs241942	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap]
rs353405	0.82[EUR][1000 genomes]
rs353406	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs353409	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs353412	0.85[EUR][1000 genomes]
rs353413	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3894129	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.80[EUR][1000 genomes]
rs4802134	1.00[CHB][hapmap]
rs4803566	0.82[EUR][1000 genomes]
rs6508752	0.80[EUR][1000 genomes]
rs697433	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs8102871	0.82[EUR][1000 genomes]
rs8110417	0.82[EUR][1000 genomes]
rs8111400	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs833916	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs861308	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949296	chr19:38034722-38763140	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs833915	PPP5C	cis	parietal	SCAN
rs833915	CEACAM16	cis	parietal	SCAN
rs833915	ZNF573	cis	brain	seeQTL
rs833915	TMEM145	cis	parietal	SCAN
rs833915	GSK3A	cis	parietal	SCAN
rs833915	ARHGEF1	cis	cerebellum	SCAN
rs833915	CD3EAP	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
3	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
4	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
8	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
11	chr19:38468200-38475600	Enhancers	HMEC	breast
12	chr19:38468200-38475800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
14	chr19:38469000-38474200	Enhancers	Fetal Intestine Large	intestine
15	chr19:38469200-38474800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
17	chr19:38469800-38475800	Genic enhancers	Fetal Intestine Small	intestine
18	chr19:38470200-38474200	Enhancers	Sigmoid Colon	Sigmoid Colon
19	chr19:38470200-38474200	Enhancers	Stomach Mucosa	stomach
20	chr19:38470200-38474400	Enhancers	Rectal Mucosa Donor 31	rectum
21	chr19:38470400-38474400	Enhancers	Esophagus	oesophagus
22	chr19:38470400-38474800	Enhancers	Gastric	stomach
23	chr19:38470600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
24	chr19:38470800-38474600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
25	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
27	chr19:38471000-38475400	Enhancers	NHEK	skin
28	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr19:38471200-38474600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
31	chr19:38471400-38476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr19:38471400-38477000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
33	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr19:38471400-38488600	Weak transcription	NHLF	lung
35	chr19:38471600-38476400	Weak transcription	Fetal Thymus	thymus
36	chr19:38471600-38477000	Weak transcription	Fetal Muscle Leg	muscle
37	chr19:38471800-38474200	Weak transcription	Brain Anterior Caudate	brain
38	chr19:38471800-38475400	Genic enhancers	Primary B cells from peripheral blood	blood
39	chr19:38472000-38474200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr19:38472000-38476400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr19:38472200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:38472200-38474200	Enhancers	Colonic Mucosa	Colon
43	chr19:38472200-38474400	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
44	chr19:38472200-38481200	Weak transcription	NHDF-Ad	bronchial
45	chr19:38472400-38474400	Weak transcription	Cortex derived primary cultured neurospheres	brain
46	chr19:38472400-38493800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
47	chr19:38472600-38480400	Enhancers	Primary B cells from cord blood	blood
48	chr19:38472600-38480400	Weak transcription	Skeletal Muscle Female	skeletal muscle
49	chr19:38472600-38481000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
50	chr19:38472800-38474200	Weak transcription	Brain Inferior Temporal Lobe	brain

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