Variant report

Variant	rs873920
Chromosome Location	chr10:95511934-95511935
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	chr10:95499932..95502310-chr10:95511778..95514024,2	MCF-7	breast:
2	chr10:95510815..95514212-chr10:95521474..95524274,4	MCF-7	breast:

Extended variants
information (count: 9 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs10736078	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10786136	0.92[CEU][hapmap];0.94[CHB][hapmap];0.82[JPT][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10882326	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.86[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4919484	0.96[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap];0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4919491	0.92[CEU][hapmap];0.94[CHB][hapmap];0.95[CHD][hapmap];0.93[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7913442	0.82[MKK][hapmap]
rs913047	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];0.90[JPT][hapmap];0.95[MEX][hapmap];0.90[TSI][hapmap];0.93[AMR][1000 genomes];0.95[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	esv3346948	chr10:95421957-95532625	Strong transcription Weak transcription Enhancers Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs873920	HECTD2	cis	cerebellum	SCAN
rs873920	FRA10AC1	cis	Artery Tibial	GTEx
rs873920	C10orf4	Cis_1M	lymphoblastoid	RTeQTL
rs873920	FRA10AC1	cis	cerebellum	SCAN
rs873920	FRA10AC1	cis	parietal	SCAN
rs873920	PLCE1	cis	hippocampus	BrainEAC
rs873920	CEP55	cis	parietal	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:95505800-95517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr10:95508200-95512800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr10:95508200-95515000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr10:95508400-95512200	Enhancers	Fetal Intestine Large	intestine
5	chr10:95508400-95512200	Enhancers	Fetal Intestine Small	intestine
6	chr10:95509200-95514600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
7	chr10:95509400-95512000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr10:95509600-95512800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
9	chr10:95509600-95514800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr10:95509800-95512200	Weak transcription	NHLF	lung
11	chr10:95509800-95514000	Weak transcription	Small Intestine	intestine
12	chr10:95510200-95512000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr10:95510200-95517600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr10:95510400-95512000	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
15	chr10:95510400-95512600	Enhancers	Placenta	Placenta
16	chr10:95510600-95512000	Enhancers	H9 Cell Line	embryonic stem cell
17	chr10:95510800-95513200	Enhancers	Hela-S3	cervix
18	chr10:95510800-95514400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr10:95511000-95512000	Active TSS	ES-I3 Cell Line	embryonic stem cell
20	chr10:95511000-95512000	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
21	chr10:95511000-95512000	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr10:95511000-95512000	Enhancers	Lung	lung
23	chr10:95511000-95512200	Enhancers	Placenta Amnion	Placenta Amnion
24	chr10:95511000-95512800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr10:95511000-95516800	Enhancers	Cortex derived primary cultured neurospheres	brain
26	chr10:95511000-95517600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
27	chr10:95511200-95512000	Enhancers	Psoas Muscle	Psoas
28	chr10:95511200-95512400	Enhancers	iPS-18 Cell Line	embryonic stem cell
29	chr10:95511200-95512600	Enhancers	Sigmoid Colon	Sigmoid Colon
30	chr10:95511200-95512800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:95511600-95512000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
32	chr10:95511600-95512000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
33	chr10:95511600-95512000	Flanking Active TSS	Adipose Nuclei	Adipose
34	chr10:95511600-95512000	Flanking Active TSS	Brain Angular Gyrus	brain
35	chr10:95511600-95512000	Flanking Active TSS	Brain Cingulate Gyrus	brain
36	chr10:95511600-95512000	Active TSS	Brain Germinal Matrix	brain
37	chr10:95511600-95512000	Flanking Active TSS	Duodenum Mucosa	Duodenum
38	chr10:95511600-95512000	Bivalent Enhancer	Fetal Kidney	kidney
39	chr10:95511600-95512000	Bivalent Enhancer	Fetal Muscle Leg	muscle
40	chr10:95511600-95512000	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
41	chr10:95511600-95512000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
42	chr10:95511600-95512000	Flanking Active TSS	Stomach Smooth Muscle	stomach
43	chr10:95511600-95512200	Bivalent Enhancer	Primary B cells from peripheral blood	blood
44	chr10:95511600-95512200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
45	chr10:95511600-95512200	Enhancers	Liver	Liver
46	chr10:95511600-95512200	Flanking Active TSS	Brain Anterior Caudate	brain
47	chr10:95511600-95512200	Active TSS	Monocytes-CD14+_RO01746	blood
48	chr10:95511600-95512600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr10:95511600-95513800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr10:95511600-95517600	Enhancers	Fetal Stomach	stomach

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