Variant report

Variant	rs2645385
Chromosome Location	chr8:20110219-20110220
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	chr8:20103827..20105570-chr8:20109022..20111621,2	MCF-7	breast:

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs11784323	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2645384	0.88[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2645386	1.00[CEU][hapmap];0.80[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2645387	1.00[ASW][hapmap];1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2645388	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2645392	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2935312	0.93[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3735839	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6586900	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs903999	0.87[JPT][hapmap]

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	nsv1033511	chr8:19751299-20625091	Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv530877	chr8:19873053-20593254	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2645385	PHYHIP	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr8:20094800-20111800	Weak transcription	Fetal Thymus	thymus
2	chr8:20096800-20119400	Weak transcription	Right Atrium	heart
3	chr8:20097200-20111800	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr8:20097400-20112400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr8:20097600-20110800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr8:20097600-20112000	Weak transcription	H1 Cell Line	embryonic stem cell
7	chr8:20102400-20118800	Weak transcription	NH-A	brain
8	chr8:20102800-20110400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr8:20103000-20111600	Strong transcription	Fetal Stomach	stomach
10	chr8:20103000-20113200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr8:20103000-20119400	Strong transcription	Dnd41	blood
12	chr8:20103200-20112600	Strong transcription	Brain Germinal Matrix	brain
13	chr8:20103200-20112800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr8:20103400-20113000	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr8:20103600-20113000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
16	chr8:20104000-20111200	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
17	chr8:20104200-20118800	Weak transcription	Fetal Intestine Large	intestine
18	chr8:20104600-20111600	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr8:20105400-20111800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr8:20105400-20114800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr8:20105800-20110400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr8:20105800-20111800	Weak transcription	Stomach Smooth Muscle	stomach
23	chr8:20106000-20114200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr8:20106200-20111600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr8:20106200-20119800	Weak transcription	Osteobl	bone
26	chr8:20106400-20111000	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr8:20106400-20113000	Strong transcription	Fetal Brain Female	brain
28	chr8:20106600-20110600	Weak transcription	Right Ventricle	heart
29	chr8:20106800-20110400	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr8:20107200-20111000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr8:20107200-20112800	Strong transcription	HSMMtube	muscle
32	chr8:20107600-20110600	Strong transcription	HSMM	muscle
33	chr8:20107800-20111800	Weak transcription	Brain Inferior Temporal Lobe	brain
34	chr8:20108200-20111200	Strong transcription	Esophagus	oesophagus
35	chr8:20108400-20111400	Strong transcription	Fetal Muscle Leg	muscle
36	chr8:20108400-20125200	Weak transcription	Fetal Intestine Small	intestine
37	chr8:20108600-20113000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
38	chr8:20108800-20110600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr8:20108800-20110800	Enhancers	Primary T killer memory cells from peripheral blood	blood
40	chr8:20108800-20110800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr8:20108800-20110800	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr8:20108800-20111200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr8:20108800-20112600	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
44	chr8:20108800-20112800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
45	chr8:20109000-20110400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
46	chr8:20109000-20110600	Enhancers	Primary T helper cells fromperipheralblood	blood
47	chr8:20109200-20110400	Strong transcription	H9 Cell Line	embryonic stem cell
48	chr8:20109200-20111600	Enhancers	Ovary	ovary
49	chr8:20109400-20110600	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
50	chr8:20109400-20112800	Strong transcription	NHLF	lung

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