Variant report

Variant	rs4470517
Chromosome Location	chr3:133882151-133882152
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	chr3:133880944..133883730-chr3:133890634..133894226,3	MCF-7	breast:
2	chr3:133874050..133876554-chr3:133881002..133883004,2	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs12493731	0.87[ASW][hapmap];0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4234422	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234423	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234424	1.00[CEU][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4234426	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4241371	1.00[JPT][hapmap]
rs4408870	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4447762	0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs4577436	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];0.87[TSI][hapmap];0.81[EUR][1000 genomes]
rs4634087	0.86[CEU][hapmap]
rs4682655	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682657	0.90[CEU][hapmap];1.00[JPT][hapmap]
rs4682665	0.95[CEU][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4682672	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4854617	0.85[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];0.89[TSI][hapmap];0.85[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854618	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854619	1.00[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.82[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4854813	0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55688777	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56104814	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56205980	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62271183	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439459	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6439467	0.88[EUR][1000 genomes]
rs6439470	0.91[CEU][hapmap];0.90[TSI][hapmap]
rs6439471	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6764932	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6779423	1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6783989	0.90[EUR][1000 genomes]
rs6787345	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6795532	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6795658	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6799962	0.90[AFR][1000 genomes];0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71807032	0.97[AMR][1000 genomes]
rs7431604	1.00[CEU][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7433368	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7611104	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7627059	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631521	0.86[EUR][1000 genomes]
rs7633386	1.00[CEU][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7634265	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9289461	1.00[CEU][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9812346	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9843401	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9862959	1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9870797	0.86[CEU][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];0.87[MEX][hapmap];0.89[TSI][hapmap];0.81[EUR][1000 genomes]
rs9883217	0.91[CEU][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4470517	EPHB1	cis	parietal	SCAN
rs4470517	IL20RB	cis	parietal	SCAN
rs4470517	ARMC8	cis	cerebellum	SCAN

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:133863000-133902200	Weak transcription	GM12878-XiMat	blood
2	chr3:133864200-133899800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:133864600-133892400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:133866200-133898600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
5	chr3:133869600-133887600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
6	chr3:133869800-133884800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
7	chr3:133870200-133885800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:133870600-133885600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr3:133870800-133885600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr3:133871800-133919200	Weak transcription	K562	blood
11	chr3:133873400-133891400	Weak transcription	Fetal Brain Female	brain
12	chr3:133873400-133907400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr3:133873600-133890400	Weak transcription	Esophagus	oesophagus
14	chr3:133873800-133892200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
15	chr3:133874400-133887800	Weak transcription	Fetal Heart	heart
16	chr3:133874400-133929400	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr3:133874600-133892200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr3:133874600-133933600	Weak transcription	Colonic Mucosa	Colon
19	chr3:133876800-133885800	Strong transcription	Primary B cells from peripheral blood	blood
20	chr3:133877600-133907400	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:133877600-133935200	Weak transcription	Psoas Muscle	Psoas
22	chr3:133877800-133884800	Weak transcription	Brain Germinal Matrix	brain
23	chr3:133877800-133885200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
24	chr3:133877800-133894200	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr3:133877800-133894400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr3:133877800-133894600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr3:133877800-133920200	Weak transcription	Brain Substantia Nigra	brain
28	chr3:133877800-133950200	Weak transcription	Small Intestine	intestine
29	chr3:133878000-133893000	Weak transcription	Primary neutrophils fromperipheralblood	blood
30	chr3:133878000-133894400	Weak transcription	NHDF-Ad	bronchial
31	chr3:133878200-133891600	Weak transcription	Brain Anterior Caudate	brain
32	chr3:133878200-133892400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
33	chr3:133878200-133892400	Weak transcription	HSMMtube	muscle
34	chr3:133878200-133893400	Weak transcription	Brain Hippocampus Middle	brain
35	chr3:133878200-133901600	Weak transcription	Fetal Brain Male	brain
36	chr3:133878400-133883000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr3:133878400-133884200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr3:133878400-133884200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr3:133878400-133884200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr3:133878400-133884400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
41	chr3:133878400-133884400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
42	chr3:133878400-133884600	Weak transcription	Stomach Smooth Muscle	stomach
43	chr3:133878400-133885200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
44	chr3:133878400-133887600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr3:133878400-133891600	Weak transcription	Skeletal Muscle Female	skeletal muscle
46	chr3:133878400-133892200	Weak transcription	Rectal Smooth Muscle	rectum
47	chr3:133878400-133893000	Weak transcription	Hela-S3	cervix
48	chr3:133878400-133894400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr3:133878400-133907400	Weak transcription	Brain Angular Gyrus	brain
50	chr3:133878600-133884200	Weak transcription	Liver	Liver

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