Variant report

Variant	rs833914
Chromosome Location	chr19:38474127-38474128
allele	C/G/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	chr19:38473416..38476574-chr19:38478709..38480543,3	MCF-7	breast:
4	chr19:38396081..38398785-chr19:38474109..38477467,3	MCF-7	breast:
5	chr19:38469123..38470666-chr19:38472308..38474390,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000105738	Chromatin interaction
ENSG00000171804	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10404567	0.80[CEU][hapmap];0.91[CHB][hapmap];0.88[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs10420746	0.80[CEU][hapmap]
rs1643462	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1643463	0.81[EUR][1000 genomes]
rs1643466	0.93[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1643467	0.86[CEU][hapmap];1.00[CHB][hapmap];0.89[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1643468	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1725469	0.92[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs1725477	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1725478	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1725480	0.81[EUR][1000 genomes]
rs1725481	0.80[CEU][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs1725482	0.80[CEU][hapmap];0.93[GIH][hapmap];0.82[LWK][hapmap];0.88[TSI][hapmap];0.96[YRI][hapmap];0.81[EUR][1000 genomes]
rs1725483	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1725485	0.81[EUR][1000 genomes]
rs1725487	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1725488	0.84[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs2075281	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap]
rs353398	0.83[ASN][1000 genomes]
rs353414	1.00[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs353415	0.80[CEU][hapmap]
rs353420	0.84[ASN][1000 genomes]
rs353423	1.00[CHB][hapmap];0.85[JPT][hapmap];0.84[ASN][1000 genomes]
rs353425	0.84[ASN][1000 genomes]
rs353430	0.81[ASN][1000 genomes]
rs4802135	0.95[CHB][hapmap];0.84[JPT][hapmap]
rs4803524	0.80[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs705492	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap]
rs705494	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.90[JPT][hapmap];0.88[TSI][hapmap]
rs705500	0.83[ASN][1000 genomes]
rs7250409	0.80[CEU][hapmap];0.95[CHB][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs752878	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8102579	0.80[CEU][hapmap];0.95[CHB][hapmap];0.86[GIH][hapmap];0.85[JPT][hapmap];0.88[TSI][hapmap]
rs8110284	0.95[CHB][hapmap];0.90[JPT][hapmap]
rs833895	1.00[CHB][hapmap];0.94[JPT][hapmap];0.96[YRI][hapmap];0.82[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833896	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs833897	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833898	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs833926	0.80[CEU][hapmap]

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

No data

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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