Variant report

Variant	rs10776776
Chromosome Location	chr1:114583160-114583161
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:114572795..114577655-chr1:114580622..114587867,10	MCF-7	breast:
2	chr1:114577897..114580371-chr1:114581560..114584344,2	MCF-7	breast:
3	chr1:114577056..114579380-chr1:114582977..114584723,3	MCF-7	breast:

Extended variants
information (count: 47 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10776777	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11102721	1.00[ASN][1000 genomes]
rs11102722	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1330700	1.00[CHB][hapmap];0.81[CHD][hapmap];0.81[MEX][hapmap];0.82[TSI][hapmap];0.83[ASN][1000 genomes]
rs1394075	0.90[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs1587773	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1604781	0.98[ASN][1000 genomes]
rs1910486	0.98[ASN][1000 genomes]
rs2938317	1.00[ASN][1000 genomes]
rs2938321	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938324	1.00[ASN][1000 genomes]
rs2938325	0.94[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938334	0.98[ASN][1000 genomes]
rs2938335	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2938336	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938337	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938338	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938339	1.00[CHB][hapmap];0.98[ASN][1000 genomes]
rs2938340	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[MEX][hapmap];0.89[TSI][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938341	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938342	0.98[ASN][1000 genomes]
rs2938343	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938344	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2938345	0.98[ASN][1000 genomes]
rs2938349	0.95[ASN][1000 genomes]
rs2938350	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2938351	0.98[ASN][1000 genomes]
rs2938353	0.83[ASN][1000 genomes]
rs3006985	0.88[ASN][1000 genomes]
rs3006986	0.88[ASN][1000 genomes]
rs3006991	0.98[ASN][1000 genomes]
rs3006992	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3006993	0.93[ASN][1000 genomes]
rs3006994	0.98[ASN][1000 genomes]
rs3006995	0.98[ASN][1000 genomes]
rs3006997	0.98[ASN][1000 genomes]
rs3007004	0.98[ASN][1000 genomes]
rs3007005	0.93[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3007007	0.98[ASN][1000 genomes]
rs3007010	0.88[ASN][1000 genomes]
rs3007013	0.83[ASN][1000 genomes]
rs514647	0.83[ASN][1000 genomes]
rs529171	0.83[ASN][1000 genomes]
rs548040	0.83[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2752424	chr1:114189958-114712958	Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
2	esv2754686	chr1:114531958-114602958	Weak transcription ZNF genes & repeats Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
3	esv1849780	chr1:114577463-114663164	Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs10776776	TSPAN2	cis	cerebellum	SCAN
rs10776776	HIGD1B	trans	brain	seeQTL
rs10776776	PHTF1	cis	cerebellum	SCAN

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:114576000-114583400	Weak transcription	Lung	lung
2	chr1:114577200-114583200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr1:114579000-114583800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr1:114580800-114583800	Enhancers	Fetal Intestine Small	intestine
5	chr1:114581200-114584800	Weak transcription	Fetal Muscle Leg	muscle
6	chr1:114581400-114583400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr1:114581600-114585400	Enhancers	Primary monocytes fromperipheralblood	blood
8	chr1:114582000-114583600	Enhancers	ES-I3 Cell Line	embryonic stem cell
9	chr1:114582000-114583600	Enhancers	HUES48 Cell Line	embryonic stem cell
10	chr1:114582000-114585400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:114582200-114585200	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:114582200-114585200	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr1:114582400-114583200	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr1:114582600-114583600	Enhancers	HMEC	breast
15	chr1:114582600-114583800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr1:114582600-114583800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr1:114582600-114584000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr1:114582600-114584000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
19	chr1:114582800-114583200	Enhancers	Muscle Satellite Cultured Cells	--
20	chr1:114582800-114583600	Bivalent Enhancer	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr1:114582800-114583600	Enhancers	Primary neutrophils fromperipheralblood	blood
22	chr1:114582800-114583800	Enhancers	HSMMtube	muscle
23	chr1:114582800-114584400	Enhancers	Fetal Intestine Large	intestine
24	chr1:114583000-114583200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
25	chr1:114583000-114590400	Weak transcription	H9 Cell Line	embryonic stem cell

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