Variant report

Variant	rs1945085
Chromosome Location	chr11:76737245-76737246
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	chr11:76730364..76733254-chr11:76737116..76739128,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000078124	Chromatin interaction

Extended variants
information (count: 25 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10899314	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11237030	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11602065	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs11605656	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12223477	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap]
rs1225138	0.80[GIH][hapmap]
rs17812687	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1945084	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2048954	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs2187499	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.98[TSI][hapmap];0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2279518	0.82[ASW][hapmap];0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap]
rs3740766	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3740768	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3862808	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4016126	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4944130	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4944133	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4945128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs55798841	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs55977032	0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs56129156	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs56789915	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs61900119	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs61900120	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7118398	0.80[AFR][1000 genomes];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs1945085	CAPN5	cis	parietal	SCAN
rs1945085	GDPD5	cis	parietal	SCAN
rs1945085	C2CD3	cis	parietal	SCAN
rs1945085	KLHL35	cis	cerebellum	SCAN
rs1945085	ACER3	cis	parietal	SCAN
rs1945085	ALG8	cis	parietal	SCAN
rs1945085	PLEKHB1	cis	cerebellum	SCAN
rs1945085	SNORD15B	cis	parietal	SCAN
rs1945085	ACER3	cis	lymphoblastoid	seeQTL

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:76694000-76738600	Weak transcription	HSMMtube	muscle
2	chr11:76696200-76738000	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr11:76701200-76738400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr11:76716400-76739800	Weak transcription	Colonic Mucosa	Colon
5	chr11:76720000-76738000	Weak transcription	Fetal Muscle Leg	muscle
6	chr11:76720400-76738000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
7	chr11:76722600-76740400	Weak transcription	Lung	lung
8	chr11:76722600-76741800	Weak transcription	Aorta	Aorta
9	chr11:76722600-76741800	Weak transcription	Gastric	stomach
10	chr11:76727200-76740400	Weak transcription	Esophagus	oesophagus
11	chr11:76730200-76738400	Weak transcription	Brain Hippocampus Middle	brain
12	chr11:76730200-76738600	Weak transcription	Brain Angular Gyrus	brain
13	chr11:76731800-76738400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr11:76732200-76738000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr11:76732200-76738600	Weak transcription	NHEK	skin
16	chr11:76732200-76741400	Weak transcription	Sigmoid Colon	Sigmoid Colon
17	chr11:76732200-76746600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr11:76732400-76737600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr11:76732400-76740000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr11:76732600-76738400	Weak transcription	HMEC	breast
21	chr11:76733000-76737800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr11:76733000-76746200	Weak transcription	Hela-S3	cervix
23	chr11:76733200-76739200	Weak transcription	Rectal Mucosa Donor 29	rectum
24	chr11:76733400-76738400	Weak transcription	Fetal Lung	lung
25	chr11:76733600-76737600	Weak transcription	Primary neutrophils fromperipheralblood	blood
26	chr11:76733600-76738400	Weak transcription	Left Ventricle	heart
27	chr11:76733600-76738600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr11:76733600-76739400	Weak transcription	Adipose Nuclei	Adipose
29	chr11:76733800-76738600	Weak transcription	Rectal Mucosa Donor 31	rectum
30	chr11:76734400-76737600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr11:76734800-76737400	Weak transcription	Monocytes-CD14+_RO01746	blood
32	chr11:76734800-76737800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr11:76734800-76746400	Weak transcription	Primary monocytes fromperipheralblood	blood
34	chr11:76735000-76737600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr11:76735400-76739000	Enhancers	Fetal Intestine Small	intestine
36	chr11:76736200-76737400	Enhancers	Stomach Mucosa	stomach
37	chr11:76736600-76737600	Enhancers	Fetal Intestine Large	intestine
38	chr11:76736600-76737800	Enhancers	A549	lung
39	chr11:76736800-76739200	Enhancers	Fetal Heart	heart
40	chr11:76737000-76737400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr11:76737200-76737400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
42	chr11:76737200-76737600	Enhancers	HepG2	liver
43	chr11:76737200-76740800	Weak transcription	Duodenum Mucosa	Duodenum

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