Variant report

Variant	rs754005
Chromosome Location	chr11:36447430-36447431
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:36440676..36443131-chr11:36444698..36447631,2	MCF-7	breast:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10836559	0.94[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10836560	0.87[ASW][hapmap];0.80[CHB][hapmap];0.86[YRI][hapmap]
rs10836561	0.87[ASW][hapmap];0.81[CHB][hapmap];0.86[YRI][hapmap]
rs11033617	0.81[ASW][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap]
rs11033619	0.80[CHB][hapmap]
rs12223629	0.82[YRI][hapmap]
rs1863397	0.81[CHB][hapmap];0.86[YRI][hapmap]
rs2422251	0.93[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs331446	0.87[CEU][hapmap];0.90[LWK][hapmap];0.90[MKK][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs577054	0.82[YRI][hapmap]
rs744895	0.94[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.92[LWK][hapmap];0.93[MEX][hapmap];0.94[MKK][hapmap];0.87[TSI][hapmap];0.95[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs744896	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.95[YRI][hapmap];0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs746762	0.93[ASW][hapmap];0.87[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.93[GIH][hapmap];0.95[JPT][hapmap];0.93[MEX][hapmap];0.80[MKK][hapmap];0.91[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs750940	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7945831	0.94[ASW][hapmap];0.81[CHB][hapmap];0.94[LWK][hapmap];0.90[MKK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs7951020	0.81[ASW][hapmap];0.82[MEX][hapmap];0.86[YRI][hapmap]
rs7952013	0.93[CEU][hapmap];0.94[CHB][hapmap];0.95[JPT][hapmap];0.95[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv467791	chr11:36108497-36999385	Flanking Active TSS Weak transcription Strong transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
2	nsv554003	chr11:36108497-36999385	ZNF genes & repeats Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs754005	EIF3M	cis	cerebellum	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:36400200-36475400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr11:36413000-36471000	Weak transcription	Aorta	Aorta
3	chr11:36414800-36475600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr11:36420400-36453200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr11:36431200-36453200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr11:36432000-36467800	Weak transcription	Esophagus	oesophagus
7	chr11:36432600-36452200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr11:36433200-36448600	Weak transcription	Rectal Smooth Muscle	rectum
9	chr11:36433400-36452600	Weak transcription	Left Ventricle	heart
10	chr11:36433800-36471400	Weak transcription	Duodenum Smooth Muscle	Duodenum
11	chr11:36435000-36447600	Weak transcription	Brain Substantia Nigra	brain
12	chr11:36435000-36448400	Weak transcription	Brain Cingulate Gyrus	brain
13	chr11:36435200-36453400	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr11:36435200-36463200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr11:36438000-36450200	Strong transcription	Sigmoid Colon	Sigmoid Colon
16	chr11:36440800-36452200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr11:36441000-36449400	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr11:36442200-36451800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
19	chr11:36442600-36449400	Weak transcription	Right Atrium	heart
20	chr11:36442600-36451200	Weak transcription	NHEK	skin
21	chr11:36442600-36462200	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:36443000-36453200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr11:36443400-36448200	Weak transcription	A549	lung
24	chr11:36443600-36448000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr11:36443600-36448600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:36443600-36449200	Weak transcription	HMEC	breast
27	chr11:36443600-36451400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
28	chr11:36443600-36451800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr11:36443600-36452600	Weak transcription	NHDF-Ad	bronchial
30	chr11:36443600-36453200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
31	chr11:36443800-36448200	Weak transcription	Osteobl	bone
32	chr11:36443800-36450200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
33	chr11:36443800-36457400	Weak transcription	Colon Smooth Muscle	Colon
34	chr11:36444000-36448000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr11:36444000-36448000	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr11:36444000-36471400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr11:36444200-36448400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr11:36444200-36448400	Weak transcription	Lung	lung
39	chr11:36444200-36471400	Weak transcription	Small Intestine	intestine
40	chr11:36444400-36447800	Weak transcription	NHLF	lung
41	chr11:36444400-36453000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr11:36444600-36447600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
43	chr11:36445400-36449600	Enhancers	Fetal Muscle Leg	muscle
44	chr11:36445600-36452400	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr11:36445800-36448400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr11:36446200-36449400	Enhancers	Fetal Lung	lung
47	chr11:36446600-36447600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr11:36446800-36447800	Enhancers	Primary T killer memory cells from peripheral blood	blood
49	chr11:36446800-36448400	Enhancers	HSMMtube	muscle
50	chr11:36446800-36448600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--

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