Variant report

Variant	rs1643459
Chromosome Location	chr19:38476173-38476174
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr19:38473416..38476574-chr19:38478709..38480543,3	MCF-7	breast:
2	chr19:38396081..38398785-chr19:38474109..38477467,3	MCF-7	breast:
3	chr19:38471726..38473895-chr19:38475514..38478507,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10853715	0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1622543	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1643455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1643456	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1643457	0.84[EUR][1000 genomes]
rs17248670	1.00[CHB][hapmap]
rs17249336	1.00[CHB][hapmap]
rs1725501	0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1725503	0.84[EUR][1000 genomes]
rs2694065	0.84[EUR][1000 genomes]
rs3859549	1.00[CHB][hapmap]
rs4536583	1.00[CHB][hapmap]
rs57733318	0.84[EUR][1000 genomes]
rs6508755	1.00[CHB][hapmap]
rs705501	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[EUR][1000 genomes]
rs705502	0.85[EUR][1000 genomes]
rs7343065	1.00[CHB][hapmap]
rs8100199	1.00[CHB][hapmap]
rs833894	0.82[EUR][1000 genomes]
rs833901	0.83[EUR][1000 genomes]
rs833902	0.84[EUR][1000 genomes]
rs833903	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs833904	0.84[EUR][1000 genomes]
rs833905	1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.84[EUR][1000 genomes]
rs833907	0.85[EUR][1000 genomes]
rs833908	0.83[EUR][1000 genomes]
rs833919	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs833920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs833921	0.83[AMR][1000 genomes];0.82[EUR][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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1643459	C19orf47	cis	parietal	SCAN
rs1643459	MEGF8	cis	cerebellum	SCAN
rs1643459	ERCC2	cis	cerebellum	SCAN
rs1643459	ZNF235	cis	cerebellum	SCAN
rs1643459	AKT2	cis	cerebellum	SCAN

Chromatin state (count:79 , 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	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
6	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
7	chr19:38468200-38483600	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr19:38469200-38479600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr19:38470800-38477200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
10	chr19:38470800-38494000	Weak transcription	Right Ventricle	heart
11	chr19:38471000-38476800	Weak transcription	HUES48 Cell Line	embryonic stem cell
12	chr19:38471200-38493800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr19:38471400-38476400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr19:38471400-38477000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr19:38471400-38483600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr19:38471400-38488600	Weak transcription	NHLF	lung
17	chr19:38471600-38476400	Weak transcription	Fetal Thymus	thymus
18	chr19:38471600-38477000	Weak transcription	Fetal Muscle Leg	muscle
19	chr19:38472000-38476400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr19:38472200-38481200	Weak transcription	NHDF-Ad	bronchial
21	chr19:38472400-38493800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
22	chr19:38472600-38480400	Enhancers	Primary B cells from cord blood	blood
23	chr19:38472600-38480400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:38472600-38481000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr19:38472800-38476800	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr19:38472800-38476800	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr19:38472800-38477000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
28	chr19:38472800-38478200	Weak transcription	Osteobl	bone
29	chr19:38472800-38489600	Weak transcription	Fetal Kidney	kidney
30	chr19:38473200-38476400	Weak transcription	Primary T cells from cord blood	blood
31	chr19:38473200-38482000	Weak transcription	Placenta Amnion	Placenta Amnion
32	chr19:38473200-38482600	Weak transcription	HSMM	muscle
33	chr19:38473200-38488600	Weak transcription	HSMMtube	muscle
34	chr19:38473600-38478200	Weak transcription	Lung	lung
35	chr19:38473600-38479400	Weak transcription	Pancreas	Pancrea
36	chr19:38473600-38480800	Weak transcription	Small Intestine	intestine
37	chr19:38473800-38476400	Weak transcription	Spleen	Spleen
38	chr19:38473800-38478200	Weak transcription	Duodenum Mucosa	Duodenum
39	chr19:38474000-38476400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr19:38474000-38477400	Enhancers	Brain Hippocampus Middle	brain
41	chr19:38474200-38476400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr19:38474200-38476600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
43	chr19:38474200-38478200	Weak transcription	Colonic Mucosa	Colon
44	chr19:38474200-38478200	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:38474400-38476400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
46	chr19:38474400-38476400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr19:38474400-38476800	Weak transcription	Rectal Mucosa Donor 29	rectum
48	chr19:38474400-38481000	Weak transcription	Esophagus	oesophagus
49	chr19:38474600-38476400	Weak transcription	H1 Cell Line	embryonic stem cell
50	chr19:38474600-38478000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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