Variant report

Variant	rs2408946
Chromosome Location	chr5:57749498-57749499
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:15)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:15 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr5:57157132..57161136-chr5:57747678..57750826,3	MCF-7	breast:
2	chr1:149221384..149225232-chr5:57748679..57751129,3	MCF-7	breast:
3	chr5:57176077..57177862-chr5:57748137..57750239,2	MCF-7	breast:
4	chr5:57490051..57491954-chr5:57748730..57750590,2	MCF-7	breast:
5	chr5:57608550..57610073-chr5:57747902..57750189,2	MCF-7	breast:
6	chr5:57538142..57540625-chr5:57748575..57750284,2	MCF-7	breast:
7	chr5:57480309..57485854-chr5:57746705..57749645,6	MCF-7	breast:
8	chr5:57708135..57711120-chr5:57747586..57749744,2	MCF-7	breast:
9	chr5:57739641..57742111-chr5:57749437..57750937,2	MCF-7	breast:
10	chr5:57555431..57557265-chr5:57747866..57749684,2	MCF-7	breast:
11	chr5:57077792..57079742-chr5:57748468..57750917,2	MCF-7	breast:
12	chr5:57471335..57473541-chr5:57748277..57749882,2	MCF-7	breast:
13	chr5:57401526..57403510-chr5:57748053..57750408,2	MCF-7	breast:
14	chr5:57370978..57374867-chr5:57746378..57750088,5	MCF-7	breast:
15	chr5:57666483..57668447-chr5:57747983..57749992,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000206737	Chromatin interaction

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs1035484	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1035485	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs1042994	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11546180	0.97[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs12513877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12513905	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518781	0.84[AFR][1000 genomes]
rs12522386	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13168504	0.87[AFR][1000 genomes]
rs13184050	0.87[AFR][1000 genomes]
rs13188849	0.87[AFR][1000 genomes]
rs16888201	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs17709855	0.94[YRI][hapmap];0.88[AFR][1000 genomes]
rs17710502	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.94[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17710615	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17767072	1.00[ASW][hapmap];1.00[CEU][hapmap];0.84[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2201293	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];0.94[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2220785	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2408947	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs33921924	1.00[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs34150563	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs34974449	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs4699926	0.87[AFR][1000 genomes]
rs4700289	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs55827457	0.95[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs56010771	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]
rs56286824	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs56318521	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59135347	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs62366360	0.88[AFR][1000 genomes]
rs6450474	0.87[AMR][1000 genomes]
rs6879330	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs6882289	0.88[AFR][1000 genomes]
rs6890785	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs72758162	0.93[EUR][1000 genomes]
rs72758173	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7701530	0.87[AFR][1000 genomes]
rs7706545	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs7708381	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7725097	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7736949	1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs929818	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2408946	IPO11	cis	cerebellum	SCAN
rs2408946	GZMK	cis	cerebellum	SCAN

Chromatin state (count:96 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:57735200-57751400	Weak transcription	Psoas Muscle	Psoas
2	chr5:57741400-57750200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr5:57742800-57750000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr5:57742800-57750800	Weak transcription	Aorta	Aorta
5	chr5:57742800-57751400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr5:57743000-57750200	Weak transcription	Pancreas	Pancrea
7	chr5:57743200-57750000	Weak transcription	NHLF	lung
8	chr5:57743800-57751000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr5:57744000-57750200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr5:57746000-57751000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr5:57746200-57749600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr5:57746200-57750200	Strong transcription	Fetal Muscle Leg	muscle
13	chr5:57746400-57750000	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr5:57746800-57749600	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr5:57746800-57750000	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr5:57746800-57750200	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr5:57746800-57750400	Weak transcription	Fetal Thymus	thymus
18	chr5:57746800-57750800	Weak transcription	Placenta Amnion	Placenta Amnion
19	chr5:57747000-57750400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr5:57747000-57752800	Weak transcription	Fetal Intestine Small	intestine
21	chr5:57747200-57750000	Weak transcription	Ovary	ovary
22	chr5:57747200-57750200	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr5:57747400-57750000	Weak transcription	Cortex derived primary cultured neurospheres	brain
24	chr5:57747400-57750000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:57747400-57750200	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
26	chr5:57747400-57750200	Weak transcription	Esophagus	oesophagus
27	chr5:57747400-57752400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr5:57747600-57749800	Weak transcription	Brain Hippocampus Middle	brain
29	chr5:57747600-57750200	Weak transcription	Gastric	stomach
30	chr5:57747600-57750200	Weak transcription	Lung	lung
31	chr5:57747800-57749600	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr5:57747800-57750000	Strong transcription	Muscle Satellite Cultured Cells	--
33	chr5:57747800-57753000	Strong transcription	Liver	Liver
34	chr5:57747800-57754200	Weak transcription	Colon Smooth Muscle	Colon
35	chr5:57748000-57749600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr5:57748000-57749600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr5:57748000-57749600	Weak transcription	Duodenum Smooth Muscle	Duodenum
38	chr5:57748000-57750000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
39	chr5:57748000-57750000	Strong transcription	HSMM	muscle
40	chr5:57748000-57750000	Strong transcription	Osteobl	bone
41	chr5:57748000-57750200	Weak transcription	Dnd41	blood
42	chr5:57748000-57752400	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr5:57748200-57751000	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr5:57748400-57749800	Genic enhancers	HMEC	breast
45	chr5:57748400-57750000	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr5:57748400-57750000	Strong transcription	Brain Germinal Matrix	brain
47	chr5:57748400-57750000	Weak transcription	Brain Substantia Nigra	brain
48	chr5:57748400-57750000	Strong transcription	Fetal Kidney	kidney
49	chr5:57748400-57750000	Genic enhancers	NHEK	skin
50	chr5:57748400-57750200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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