Variant report

Variant	rs836788
Chromosome Location	chr5:79912044-79912045
allele	A/G
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:
2	chr5:79911558..79913101-chr5:79913711..79915677,2	K562	blood:

Extended variants
information (count: 17 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs1232027	0.84[MKK][hapmap]
rs12517451	0.87[CHB][hapmap];0.88[CHD][hapmap]
rs1643665	0.91[ASN][1000 genomes]
rs1650697	0.87[CHB][hapmap];0.85[CHD][hapmap]
rs2115014	0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[ASN][1000 genomes]
rs2434329	0.81[ASN][1000 genomes]
rs372069	0.83[ASN][1000 genomes]
rs380691	0.83[CHB][hapmap];0.82[CHD][hapmap];0.90[JPT][hapmap]
rs384925	0.83[ASN][1000 genomes]
rs425463	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs431443	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443611	0.83[ASN][1000 genomes]
rs525054	0.81[ASN][1000 genomes]
rs836805	0.83[CHB][hapmap];0.87[JPT][hapmap]
rs861365	0.83[ASN][1000 genomes]
rs863901	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[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
rs836788	MSH3	cis	cerebellum	SCAN
rs836788	MSH3	cis	Adipose Subcutaneous	GTEx
rs836788	MSH3	cis	Whole Blood	GTEx
rs836788	MSH3	cis	Thyroid	GTEx
rs836788	MSH3	cis	parietal	SCAN

Chromatin state (count:27 , 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	chr5:79909400-79916200	Weak transcription	Primary neutrophils fromperipheralblood	blood
6	chr5:79909800-79927200	Weak transcription	Primary T cells from cord blood	blood
7	chr5:79910200-79913400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr5:79910600-79927000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:79911400-79912200	Active TSS	Brain Inferior Temporal Lobe	brain
10	chr5:79911400-79912200	Active TSS	Brain Substantia Nigra	brain
11	chr5:79911600-79912200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:79911600-79913600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr5:79911600-79925400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr5:79911600-79925400	Weak transcription	Adipose Nuclei	Adipose
15	chr5:79911800-79912200	Enhancers	Breast Myoepithelial Primary Cells	Breast
16	chr5:79911800-79912200	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr5:79911800-79912600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr5:79911800-79913400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr5:79911800-79913600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr5:79911800-79915800	Weak transcription	NH-A	brain
21	chr5:79911800-79916200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr5:79911800-79916200	Weak transcription	Placenta Amnion	Placenta Amnion
23	chr5:79911800-79925200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr5:79911800-79927200	Weak transcription	HMEC	breast
25	chr5:79912000-79926400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr5:79912000-79926600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr5:79912000-79938000	Weak transcription	Brain Anterior Caudate	brain

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