Variant report

Variant	rs833898
Chromosome Location	chr19:38469084-38469085
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:38463904..38465863-chr19:38467439..38469281,2	MCF-7	breast:

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10404567	1.00[CEU][hapmap];0.91[CHB][hapmap];0.94[JPT][hapmap];0.85[EUR][1000 genomes]
rs10415548	0.83[CEU][hapmap]
rs10420746	1.00[CEU][hapmap]
rs1119229	0.88[CEU][hapmap]
rs1643462	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1643463	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1643466	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643467	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643468	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1643469	0.95[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs1725469	0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1725477	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1725478	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1725480	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725481	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725482	1.00[CEU][hapmap];0.84[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725483	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725485	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1725487	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1725488	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725494	0.92[EUR][1000 genomes]
rs1725499	0.83[CEU][hapmap]
rs2075281	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2544718	0.92[EUR][1000 genomes]
rs35209753	0.83[EUR][1000 genomes]
rs353398	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs353399	0.95[EUR][1000 genomes]
rs353400	0.95[EUR][1000 genomes]
rs353402	0.95[EUR][1000 genomes]
rs353403	0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs353404	0.95[EUR][1000 genomes]
rs353407	0.95[EUR][1000 genomes]
rs353410	0.83[CEU][hapmap]
rs353411	0.83[CEU][hapmap]
rs353414	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs353415	1.00[CEU][hapmap];0.84[JPT][hapmap];0.92[EUR][1000 genomes]
rs353416	0.95[EUR][1000 genomes]
rs353417	0.95[EUR][1000 genomes]
rs353419	0.95[EUR][1000 genomes]
rs353420	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353421	0.95[EUR][1000 genomes]
rs353423	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353424	0.95[EUR][1000 genomes]
rs353425	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs353426	0.93[EUR][1000 genomes]
rs353427	0.95[EUR][1000 genomes]
rs353428	0.91[EUR][1000 genomes]
rs353429	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs353430	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3786869	0.83[CEU][hapmap]
rs4239516	0.83[CEU][hapmap]
rs4802135	0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4803524	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs4803551	0.88[CEU][hapmap]
rs4803573	0.88[CEU][hapmap]
rs705491	0.88[CEU][hapmap]
rs705492	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs705493	0.88[CEU][hapmap]
rs705494	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs705495	0.88[CEU][hapmap]
rs705500	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7250409	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap];0.86[EUR][1000 genomes]
rs7258597	0.85[EUR][1000 genomes]
rs752878	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8102579	1.00[CEU][hapmap];0.95[CHB][hapmap];0.94[JPT][hapmap]
rs8107341	0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8110284	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs8113521	0.83[CEU][hapmap]
rs833895	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833896	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs833914	0.80[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833926	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs9304572	0.86[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs833898	WDR87	cis	Thyroid	GTEx
rs833898	ZNF571	cis	multi-tissue	Pritchard

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:38457200-38470400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr19:38457600-38470200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr19:38457600-38470400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr19:38457600-38470400	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr19:38461600-38470200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr19:38461600-38470200	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr19:38461600-38470200	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr19:38461600-38470400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
10	chr19:38461600-38470400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr19:38461600-38470400	Weak transcription	Gastric	stomach
12	chr19:38461600-38472000	Weak transcription	NHDF-Ad	bronchial
13	chr19:38461600-38476600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr19:38461600-38493600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr19:38461600-38493600	Weak transcription	Stomach Smooth Muscle	stomach
16	chr19:38461800-38470600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr19:38461800-38476800	Weak transcription	H9 Cell Line	embryonic stem cell
18	chr19:38462000-38470200	Weak transcription	Duodenum Mucosa	Duodenum
19	chr19:38462200-38470800	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr19:38462200-38471800	Enhancers	Primary B cells from peripheral blood	blood
21	chr19:38463400-38470400	Weak transcription	Colonic Mucosa	Colon
22	chr19:38463600-38476000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr19:38463800-38476200	Weak transcription	Primary hematopoietic stem cells	blood
24	chr19:38463800-38484800	Weak transcription	Fetal Stomach	stomach
25	chr19:38464000-38470400	Weak transcription	Fetal Muscle Leg	muscle
26	chr19:38464200-38469800	Strong transcription	Fetal Intestine Small	intestine
27	chr19:38465200-38470200	Weak transcription	Liver	Liver
28	chr19:38466000-38470200	Weak transcription	Stomach Mucosa	stomach
29	chr19:38466000-38472400	Weak transcription	Primary T cells from cord blood	blood
30	chr19:38466000-38475800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr19:38466200-38469600	Weak transcription	HepG2	liver
32	chr19:38467800-38471800	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr19:38468000-38469200	Enhancers	Brain Angular Gyrus	brain
34	chr19:38468000-38472000	Enhancers	Primary B cells from cord blood	blood
35	chr19:38468200-38469200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr19:38468200-38469200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr19:38468200-38469200	Enhancers	Muscle Satellite Cultured Cells	--
38	chr19:38468200-38469200	Enhancers	Brain Anterior Caudate	brain
39	chr19:38468200-38469200	Enhancers	Brain Hippocampus Middle	brain
40	chr19:38468200-38469200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
41	chr19:38468200-38469200	Enhancers	Brain Substantia Nigra	brain
42	chr19:38468200-38469600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
43	chr19:38468200-38469600	Enhancers	Brain Inferior Temporal Lobe	brain
44	chr19:38468200-38470200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr19:38468200-38470600	Enhancers	NHEK	skin
46	chr19:38468200-38471200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr19:38468200-38473600	Enhancers	Lung	lung
48	chr19:38468200-38474200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr19:38468200-38474600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr19:38468200-38475600	Enhancers	HMEC	breast

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