Variant report

Variant	rs10445895
Chromosome Location	chr2:58390538-58390539
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	chr2:58382472..58384235-chr2:58388859..58391605,2	MCF-7	breast:

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10445896	0.89[CEU][hapmap];0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17049270	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17049296	0.81[CEU][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.81[EUR][1000 genomes]
rs17049298	0.81[CEU][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes]
rs17049318	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17049334	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17049339	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.86[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17049351	1.00[ASW][hapmap];0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs17049366	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2196806	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771204	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771206	0.81[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771211	1.00[ASW][hapmap];0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs3771212	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56246409	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57471952	0.81[EUR][1000 genomes]
rs59378271	0.81[EUR][1000 genomes]
rs60152647	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs73942293	0.83[EUR][1000 genomes]
rs7577299	0.81[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv525988	chr2:58161520-58427786	Enhancers Weak transcription Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv999042	chr2:58326123-58530903	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
3	nsv535734	chr2:58326123-58530903	ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv1007527	chr2:58386271-58477536	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
5	nsv535735	chr2:58386271-58477536	Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
6	nsv458052	chr2:58388696-58450569	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
7	nsv582098	chr2:58388696-58450569	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
8	nsv817995	chr2:58390538-58450569	Enhancers ZNF genes & repeats Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10445895	PUS10	cis	cerebellum	SCAN

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:58349000-58421200	Weak transcription	Brain Substantia Nigra	brain
2	chr2:58358200-58393800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr2:58359000-58391400	Weak transcription	Fetal Muscle Leg	muscle
4	chr2:58359000-58399000	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr2:58359000-58454000	Weak transcription	Stomach Smooth Muscle	stomach
6	chr2:58359200-58395200	Weak transcription	Fetal Stomach	stomach
7	chr2:58359200-58399200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
8	chr2:58359800-58392000	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr2:58363400-58399000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr2:58363600-58406800	Weak transcription	Brain Hippocampus Middle	brain
11	chr2:58365600-58438000	Weak transcription	Brain Cingulate Gyrus	brain
12	chr2:58368200-58403000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr2:58368200-58417000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr2:58368600-58399000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr2:58374400-58393400	Weak transcription	NHEK	skin
16	chr2:58374400-58397400	Weak transcription	Fetal Heart	heart
17	chr2:58380800-58398800	Weak transcription	Spleen	Spleen
18	chr2:58381000-58398800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr2:58381200-58391600	Weak transcription	Brain Inferior Temporal Lobe	brain
20	chr2:58382200-58393200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr2:58382400-58391800	Strong transcription	Dnd41	blood
22	chr2:58382600-58390600	Strong transcription	Liver	Liver
23	chr2:58382600-58391400	Weak transcription	Brain Angular Gyrus	brain
24	chr2:58382600-58394000	Weak transcription	Fetal Brain Male	brain
25	chr2:58382600-58395400	Weak transcription	Pancreas	Pancrea
26	chr2:58382600-58395800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:58382600-58400200	Weak transcription	Brain Germinal Matrix	brain
28	chr2:58382600-58400400	Weak transcription	Gastric	stomach
29	chr2:58382800-58394400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr2:58382800-58395800	Weak transcription	Lung	lung
31	chr2:58382800-58398800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr2:58382800-58398800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
33	chr2:58382800-58399000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr2:58383000-58415600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr2:58383200-58391800	Weak transcription	Colon Smooth Muscle	Colon
36	chr2:58383200-58398800	Weak transcription	Esophagus	oesophagus
37	chr2:58383200-58415000	Weak transcription	Rectal Smooth Muscle	rectum
38	chr2:58383800-58390800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr2:58384000-58393800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr2:58384200-58392200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr2:58384200-58394800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr2:58384400-58390600	Strong transcription	HepG2	liver
43	chr2:58384400-58391800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr2:58384400-58391800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr2:58384400-58392200	Strong transcription	HUES6 Cell Line	embryonic stem cell
46	chr2:58384600-58390800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr2:58384600-58393000	Strong transcription	HUES48 Cell Line	embryonic stem cell
48	chr2:58384600-58393000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
49	chr2:58384600-58393000	Weak transcription	Skeletal Muscle Male	skeletal muscle
50	chr2:58384800-58395400	Weak transcription	Aorta	Aorta

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