Variant report

Variant	rs10858004
Chromosome Location	chr1:114092306-114092307
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	chr1:114084981..114088872-chr1:114091176..114094977,3	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs11102660	0.82[CEU][hapmap];1.00[TSI][hapmap];0.86[EUR][1000 genomes]
rs11588901	0.82[EUR][1000 genomes]
rs11802041	1.00[CHD][hapmap];1.00[JPT][hapmap]
rs12026423	0.87[CEU][hapmap];0.81[GIH][hapmap];0.88[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs12065882	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12119076	0.86[ASN][1000 genomes]
rs12129076	0.86[ASN][1000 genomes]
rs1343126	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs7515189	0.96[TSI][hapmap]
rs7518766	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv437013	chr1:114065955-114129092	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Genic enhancers Active TSS	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
2	nsv947128	chr1:114088844-114122533	ZNF genes & repeats Weak transcription Strong transcription Enhancers Genic enhancers Active TSS Flanking Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10858004	PHTF1	cis	parietal	SCAN
rs10858004	MAGI3	cis	cerebellum	SCAN
rs10858004	GADD45A	trans	lymphoblastoid	seeQTL

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114072200-114095800	Weak transcription	Aorta	Aorta
2	chr1:114082600-114100400	Weak transcription	Fetal Kidney	kidney
3	chr1:114083200-114099800	Weak transcription	Pancreas	Pancrea
4	chr1:114083400-114095200	Weak transcription	Liver	Liver
5	chr1:114083400-114100000	Weak transcription	Ovary	ovary
6	chr1:114083400-114110000	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr1:114084800-114095200	Weak transcription	Fetal Intestine Large	intestine
8	chr1:114084800-114095600	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr1:114085000-114092400	Weak transcription	Fetal Intestine Small	intestine
10	chr1:114085600-114093600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:114085600-114094000	Weak transcription	HMEC	breast
12	chr1:114085600-114094200	Weak transcription	NHDF-Ad	bronchial
13	chr1:114085600-114101800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:114088200-114102000	Weak transcription	Colon Smooth Muscle	Colon
15	chr1:114088600-114099600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr1:114088600-114101000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr1:114088600-114109800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr1:114088800-114093800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr1:114088800-114094200	Weak transcription	NHEK	skin
20	chr1:114090400-114093000	Weak transcription	HepG2	liver
21	chr1:114090400-114099800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
22	chr1:114090800-114093600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr1:114091000-114093600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
24	chr1:114091000-114099800	Weak transcription	Left Ventricle	heart
25	chr1:114091200-114093600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:114091200-114093600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
27	chr1:114091200-114101800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr1:114091600-114093600	Weak transcription	HUES48 Cell Line	embryonic stem cell
29	chr1:114092000-114092400	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr1:114092000-114099600	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr1:114092200-114099200	Weak transcription	Breast Myoepithelial Primary Cells	Breast

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