Variant report

Variant	rs2767515
Chromosome Location	chr1:56165742-56165743
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:56164134..56166630-chr1:56174499..56177459,2	MCF-7	breast:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs11206659	0.85[ASN][1000 genomes]
rs1165478	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1165480	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1165481	0.92[CEU][hapmap];0.90[EUR][1000 genomes]
rs1165482	0.89[EUR][1000 genomes]
rs1165483	0.92[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs1165484	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1165485	0.81[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs1165486	0.92[CEU][hapmap];0.81[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs1182821	1.00[CHB][hapmap];0.92[JPT][hapmap];0.98[ASN][1000 genomes]
rs1183736	0.92[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12036264	0.85[ASN][1000 genomes]
rs12407237	0.86[ASN][1000 genomes]
rs1514141	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1514142	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1514146	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1877716	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1877717	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1955318	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs2255776	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2671226	0.87[CEU][hapmap];0.83[EUR][1000 genomes]
rs2671227	0.92[ASN][1000 genomes]
rs2671228	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2671229	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2671231	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2671232	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2671233	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2671234	0.92[CEU][hapmap];0.86[CHB][hapmap];0.85[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2671237	0.92[CEU][hapmap];0.89[TSI][hapmap];0.89[EUR][1000 genomes]
rs2671238	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.82[YRI][hapmap];0.92[ASN][1000 genomes]
rs2671239	0.92[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2671240	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2671241	0.95[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2671242	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2671245	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];1.00[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2767502	0.89[ASN][1000 genomes]
rs2767503	0.92[CEU][hapmap];0.85[CHD][hapmap];0.93[JPT][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2767504	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2767507	0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2767508	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2767509	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2767510	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2767513	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2767514	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2767516	0.92[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2767518	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2767519	0.91[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819472	0.95[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs2819473	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2819474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2819476	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2819477	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2819479	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2819482	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819487	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819488	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819489	0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819490	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2819491	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs3914413	0.90[ASN][1000 genomes]
rs4367813	0.90[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs748284	0.92[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9326036	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9436520	0.83[CHD][hapmap];0.93[JPT][hapmap]
rs9436521	0.85[ASN][1000 genomes]
rs9436522	0.93[CHB][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs9436524	0.85[ASN][1000 genomes]
rs9436525	0.85[ASN][1000 genomes]
rs9436526	0.90[CHB][hapmap];0.93[JPT][hapmap];0.85[ASN][1000 genomes]
rs9436981	0.85[ASN][1000 genomes]
rs9436984	0.90[CHB][hapmap];0.93[JPT][hapmap];0.81[YRI][hapmap];0.90[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2767515	MYSM1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56158400-56170800	Enhancers	NHDF-Ad	bronchial
2	chr1:56159600-56166800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr1:56161400-56165800	Weak transcription	Rectal Smooth Muscle	rectum
4	chr1:56161400-56169400	Weak transcription	Placenta	Placenta
5	chr1:56161600-56165800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr1:56162400-56166000	Weak transcription	HSMM	muscle
7	chr1:56162400-56169400	Weak transcription	Ovary	ovary
8	chr1:56162600-56166200	Weak transcription	HSMMtube	muscle
9	chr1:56162800-56165800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr1:56162800-56165800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr1:56163000-56165800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr1:56163000-56166000	Weak transcription	NH-A	brain
13	chr1:56163400-56166200	Weak transcription	Fetal Stomach	stomach
14	chr1:56163800-56165800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
15	chr1:56164400-56167200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr1:56164400-56167800	Enhancers	NHLF	lung
17	chr1:56164600-56166800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr1:56164800-56167000	Enhancers	Muscle Satellite Cultured Cells	--
19	chr1:56164800-56169000	Weak transcription	Fetal Lung	lung
20	chr1:56165000-56167000	Enhancers	Colon Smooth Muscle	Colon
21	chr1:56165200-56166000	Weak transcription	A549	lung
22	chr1:56165400-56167000	Enhancers	Osteobl	bone
23	chr1:56165600-56167400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin

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