Variant report

Variant	rs39967
Chromosome Location	chr5:57744788-57744789
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:57736186..57738173-chr5:57743943..57745504,2	MCF-7	breast:
2	chr5:57342588..57345255-chr5:57743719..57745899,2	MCF-7	breast:
3	chr5:57662265..57664102-chr5:57743595..57746486,2	MCF-7	breast:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs10051454	1.00[AFR][1000 genomes]
rs10057291	0.83[AFR][1000 genomes]
rs10065306	0.83[AFR][1000 genomes]
rs10070159	0.83[AFR][1000 genomes]
rs10940616	0.83[AFR][1000 genomes]
rs13173334	1.00[AFR][1000 genomes]
rs13174658	0.83[AFR][1000 genomes]
rs13184329	1.00[AFR][1000 genomes]
rs150249	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs150271	0.94[ASN][1000 genomes]
rs151890	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs151893	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs154472	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154474	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154491	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs154492	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs154493	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs158154	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158158	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158159	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158280	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs158281	0.94[CEU][hapmap];0.92[MEX][hapmap];0.81[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17773723	0.83[AFR][1000 genomes]
rs17773753	0.83[AFR][1000 genomes]
rs2591919	1.00[ASW][hapmap]
rs32613	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs32614	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs41088	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs42739	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs42740	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67873319	0.83[AFR][1000 genomes]
rs697134	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702709	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs702710	0.97[ASN][1000 genomes]
rs702717	0.97[ASN][1000 genomes]
rs702720	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs702721	1.00[ASN][1000 genomes]
rs702723	0.86[CHD][hapmap];0.82[JPT][hapmap]
rs832631	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs832636	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs39967	GZMK	cis	cerebellum	SCAN

Chromatin state (count:38 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57735200-57751400	Weak transcription	Psoas Muscle	Psoas
2	chr5:57737000-57747400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr5:57737400-57747000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr5:57737800-57748600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr5:57737800-57749000	Weak transcription	Fetal Lung	lung
6	chr5:57741200-57744800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr5:57741200-57745200	Weak transcription	NHEK	skin
8	chr5:57741200-57747000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr5:57741400-57746000	Weak transcription	Fetal Muscle Trunk	muscle
10	chr5:57741400-57750200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr5:57741600-57745800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr5:57741600-57747200	Weak transcription	Esophagus	oesophagus
13	chr5:57742200-57747800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr5:57742400-57745000	Weak transcription	Fetal Muscle Leg	muscle
15	chr5:57742600-57746200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr5:57742600-57747400	Weak transcription	Fetal Brain Female	brain
17	chr5:57742800-57750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
18	chr5:57742800-57750800	Weak transcription	Aorta	Aorta
19	chr5:57742800-57751400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr5:57743000-57746000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr5:57743000-57748800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr5:57743000-57749400	Weak transcription	NHDF-Ad	bronchial
23	chr5:57743000-57750200	Weak transcription	Pancreas	Pancrea
24	chr5:57743200-57746000	Weak transcription	HMEC	breast
25	chr5:57743200-57746200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
26	chr5:57743200-57748400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr5:57743200-57750000	Weak transcription	NHLF	lung
28	chr5:57743400-57745400	Weak transcription	A549	lung
29	chr5:57743600-57746000	Weak transcription	Muscle Satellite Cultured Cells	--
30	chr5:57743600-57746000	Weak transcription	Liver	Liver
31	chr5:57743600-57746200	Weak transcription	NH-A	brain
32	chr5:57743600-57746200	Weak transcription	Osteobl	bone
33	chr5:57743600-57748000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr5:57743800-57748000	Weak transcription	HSMM	muscle
35	chr5:57743800-57748400	Weak transcription	Fetal Kidney	kidney
36	chr5:57743800-57751000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
37	chr5:57744000-57750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
38	chr5:57744400-57749200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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