Variant report

Variant	rs10769990
Chromosome Location	chr11:9145807-9145808
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr11:9131112..9133344-chr11:9145799..9148369,2	MCF-7	breast:
2	chr11:9143576..9146449-chr11:9146558..9148166,2	MCF-7	breast:

Extended variants
information (count: 5 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1827011	0.88[LWK][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes]
rs7395347	0.89[LWK][hapmap];0.81[YRI][hapmap];0.81[AFR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3413845	chr11:8887279-9285127	Enhancers Transcr. at gene 5' and 3' Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	esv33264	chr11:9007612-9311131	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
3	nsv896985	chr11:9013002-9152463	Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	18 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10769990	OR5P2	cis	parietal	SCAN
rs10769990	ILK	cis	parietal	SCAN
rs10769990	TRIM5	cis	cerebellum	SCAN
rs10769990	CNGA4	cis	cerebellum	SCAN

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:9113600-9159800	Weak transcription	Right Ventricle	heart
2	chr11:9121800-9154800	Weak transcription	Brain Substantia Nigra	brain
3	chr11:9130800-9153600	Weak transcription	Brain Angular Gyrus	brain
4	chr11:9132000-9153200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
5	chr11:9134000-9153000	Weak transcription	Brain Germinal Matrix	brain
6	chr11:9134000-9154000	Weak transcription	Osteobl	bone
7	chr11:9134200-9154000	Weak transcription	NHDF-Ad	bronchial
8	chr11:9134800-9159000	Weak transcription	Brain Hippocampus Middle	brain
9	chr11:9134800-9161200	Weak transcription	Fetal Brain Male	brain
10	chr11:9135200-9152600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr11:9135600-9153000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr11:9136400-9159200	Weak transcription	Brain Anterior Caudate	brain
13	chr11:9137200-9159000	Weak transcription	Fetal Heart	heart
14	chr11:9137800-9146200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr11:9141200-9153000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr11:9141400-9151800	Weak transcription	Psoas Muscle	Psoas
17	chr11:9141400-9153600	Weak transcription	Primary T cells from cord blood	blood
18	chr11:9141400-9153800	Weak transcription	Brain Inferior Temporal Lobe	brain
19	chr11:9141600-9151800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr11:9141600-9158400	Weak transcription	Pancreas	Pancrea
21	chr11:9142000-9148400	Weak transcription	Right Atrium	heart
22	chr11:9142000-9157200	Weak transcription	NHLF	lung
23	chr11:9142400-9163000	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr11:9142600-9153000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr11:9142600-9159000	Weak transcription	Adipose Nuclei	Adipose
26	chr11:9142600-9159200	Weak transcription	Duodenum Mucosa	Duodenum
27	chr11:9142600-9175000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
28	chr11:9143000-9152600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
29	chr11:9143000-9154400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr11:9143000-9155000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr11:9143400-9149400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr11:9143400-9152000	Weak transcription	Left Ventricle	heart
33	chr11:9143400-9159200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr11:9143400-9161200	Weak transcription	Aorta	Aorta
35	chr11:9143600-9148400	Weak transcription	HUES64 Cell Line	embryonic stem cell
36	chr11:9143600-9150200	Weak transcription	HSMM	muscle
37	chr11:9143600-9151800	Weak transcription	Fetal Muscle Trunk	muscle
38	chr11:9143600-9152600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr11:9143600-9152800	Weak transcription	HUES6 Cell Line	embryonic stem cell
40	chr11:9143600-9159000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:9143800-9148200	Weak transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:9143800-9148400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
43	chr11:9143800-9152000	Weak transcription	Fetal Stomach	stomach
44	chr11:9143800-9152600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
45	chr11:9143800-9158800	Weak transcription	Fetal Brain Female	brain
46	chr11:9144000-9151800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
47	chr11:9144400-9161200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr11:9144800-9153400	Weak transcription	Cortex derived primary cultured neurospheres	brain
49	chr11:9145400-9156800	Weak transcription	Placenta	Placenta
50	chr11:9145800-9146000	ZNF genes & repeats	Fetal Muscle Leg	muscle

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