Variant report

Variant	rs259358
Chromosome Location	chr1:95709821-95709822
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	chr1:95699987..95702820-chr1:95708851..95710565,2	MCF-7	breast:
2	chr1:95705493..95708306-chr1:95709023..95711361,3	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10458507	0.88[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs10747465	1.00[AMR][1000 genomes]
rs10783000	1.00[AMR][1000 genomes]
rs11165298	1.00[JPT][hapmap]
rs11165320	1.00[YRI][hapmap]
rs12098237	1.00[AMR][1000 genomes]
rs1336438	1.00[AMR][1000 genomes]
rs1998967	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs59828565	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs613351	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6593614	1.00[AMR][1000 genomes]
rs6593615	0.82[YRI][hapmap];1.00[AMR][1000 genomes]
rs6593619	0.86[LWK][hapmap];1.00[MEX][hapmap];1.00[AMR][1000 genomes]
rs6659370	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs7365394	0.93[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap]
rs7366061	1.00[AMR][1000 genomes]
rs7516500	1.00[AMR][1000 genomes]
rs7520889	0.94[LWK][hapmap]
rs7540042	1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes]

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs259358	MYO6	trans	lymphoblastoid	seeQTL
rs259358	T	trans	lymphoblastoid	seeQTL
rs259358	ADAM23	trans	lymphoblastoid	seeQTL
rs259358	VIM	trans	lymphoblastoid	seeQTL
rs259358	RWDD3	cis	lymphoblastoid	seeQTL

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:95700600-95712000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
2	chr1:95700600-95713200	Weak transcription	HMEC	breast
3	chr1:95700600-95715000	Weak transcription	HUVEC	blood vessel
4	chr1:95700600-95719800	Weak transcription	NHDF-Ad	bronchial
5	chr1:95702600-95719800	Weak transcription	Colon Smooth Muscle	Colon
6	chr1:95703400-95719000	Weak transcription	Small Intestine	intestine
7	chr1:95703600-95716200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
8	chr1:95703600-95720800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr1:95703800-95716400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr1:95704200-95715400	Weak transcription	Psoas Muscle	Psoas
11	chr1:95705000-95710200	Strong transcription	Fetal Intestine Large	intestine
12	chr1:95705000-95710800	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:95705200-95710200	Strong transcription	Stomach Smooth Muscle	stomach
14	chr1:95705200-95710400	Strong transcription	Primary B cells from peripheral blood	blood
15	chr1:95705200-95715200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr1:95705400-95710000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr1:95705400-95710200	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr1:95705400-95710200	Strong transcription	Rectal Mucosa Donor 29	rectum
19	chr1:95705400-95710400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:95705400-95710400	Strong transcription	Osteobl	bone
21	chr1:95705600-95710600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr1:95705600-95710600	Strong transcription	Placenta	Placenta
23	chr1:95705600-95710800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr1:95705600-95720800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr1:95706800-95712200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr1:95707000-95719000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr1:95707200-95710400	Strong transcription	Primary T cells from cord blood	blood
28	chr1:95707200-95715200	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr1:95707200-95717800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr1:95707400-95710400	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr1:95707400-95712200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr1:95707400-95714400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr1:95707400-95714800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:95707400-95717800	Weak transcription	Esophagus	oesophagus
35	chr1:95707400-95719200	Weak transcription	Spleen	Spleen
36	chr1:95707400-95719600	Weak transcription	Lung	lung
37	chr1:95707400-95719800	Weak transcription	Gastric	stomach
38	chr1:95707400-95720200	Weak transcription	HSMMtube	muscle
39	chr1:95707400-95722600	Weak transcription	Aorta	Aorta
40	chr1:95707400-95722800	Weak transcription	Pancreas	Pancrea
41	chr1:95707400-95727600	Weak transcription	Brain Angular Gyrus	brain
42	chr1:95707600-95714400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr1:95707600-95716000	Weak transcription	Colonic Mucosa	Colon
44	chr1:95707600-95717600	Weak transcription	GM12878-XiMat	blood
45	chr1:95707600-95720000	Weak transcription	Muscle Satellite Cultured Cells	--
46	chr1:95707800-95710200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
47	chr1:95707800-95710800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr1:95707800-95714400	Weak transcription	Fetal Stomach	stomach
49	chr1:95707800-95714800	Weak transcription	Thymus	Thymus
50	chr1:95707800-95715200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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