Variant report

Variant	rs1643665
Chromosome Location	chr5:79910843-79910844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:79910821..79913397-chr5:79915125..79917648,2	MCF-7	breast:

Extended variants
information (count: 16 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1105524	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2115014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2434329	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs372069	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs380691	1.00[CEU][hapmap];0.91[CHB][hapmap];0.98[CHD][hapmap];0.96[GIH][hapmap];0.95[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs384925	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs425463	0.91[CHB][hapmap];0.84[CHD][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs431443	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs442767	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs443611	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs525054	0.91[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs836788	0.91[ASN][1000 genomes]
rs836805	0.82[JPT][hapmap]
rs861365	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs863901	0.91[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	nsv1024844	chr5:79862428-80860430	Weak transcription Strong transcription Enhancers Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs1643665	DHFR	Cis_1M	lymphoblastoid	RTeQTL
rs1643665	MSH3	Cis_1M	lymphoblastoid	RTeQTL
rs1643665	DHFR///LOC643509	Cis_1M	lymphoblastoid	RTeQTL
rs1643665	DHFR	cis	Esophagus Muscularis	GTEx
rs1643665	DHFR	cis	Muscle Skeletal	GTEx

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:79902400-79916600	Weak transcription	Thymus	Thymus
2	chr5:79904000-79914400	Weak transcription	Dnd41	blood
3	chr5:79904800-79925000	Weak transcription	Primary B cells from cord blood	blood
4	chr5:79906600-79949200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr5:79907000-79911000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:79908800-79911000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr5:79909400-79916200	Weak transcription	Primary neutrophils fromperipheralblood	blood
8	chr5:79909800-79927200	Weak transcription	Primary T cells from cord blood	blood
9	chr5:79910200-79911200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr5:79910200-79913400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr5:79910400-79911400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr5:79910600-79911000	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr5:79910600-79927000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr5:79910800-79911000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr5:79910800-79911000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr5:79910800-79911200	Enhancers	iPS-15b Cell Line	embryonic stem cell
17	chr5:79910800-79911200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
18	chr5:79910800-79911200	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr5:79910800-79911800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr5:79910800-79912000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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