Variant report

Variant	rs10899923
Chromosome Location	chr10:44357854-44357855
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	chr10:44351789..44354047-chr10:44357316..44359324,2	MCF-7	breast:

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs1008803	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1009769	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1009770	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1009771	0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10899925	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899927	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10899928	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10899929	0.85[EUR][1000 genomes]
rs10899932	0.81[EUR][1000 genomes]
rs10899944	0.81[EUR][1000 genomes]
rs11238741	0.85[EUR][1000 genomes]
rs11238749	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11238750	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11238753	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11238754	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11238755	0.85[EUR][1000 genomes]
rs11238756	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11238759	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11238761	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11238764	0.80[EUR][1000 genomes]
rs12359360	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1468061	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17464560	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2031513	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2169200	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4948580	0.93[EUR][1000 genomes]
rs4948581	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4948786	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56034709	0.80[EUR][1000 genomes]
rs7903927	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7909314	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs881714	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs912805	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9633744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10899923	LINC00840	cis	lung	GTEx
rs10899923	LOC338579	cis	cerebellum	SCAN

Chromatin state (count:39 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44351400-44358000	Weak transcription	Adipose Nuclei	Adipose
2	chr10:44352000-44359200	Weak transcription	Fetal Heart	heart
3	chr10:44353000-44359600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr10:44353200-44358200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr10:44353400-44358400	Weak transcription	Fetal Stomach	stomach
6	chr10:44353400-44358400	Weak transcription	Gastric	stomach
7	chr10:44353400-44358800	Weak transcription	Fetal Muscle Trunk	muscle
8	chr10:44353400-44358800	Weak transcription	Pancreas	Pancrea
9	chr10:44353600-44359600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr10:44356800-44361200	Enhancers	NHDF-Ad	bronchial
11	chr10:44357000-44358000	Enhancers	Sigmoid Colon	Sigmoid Colon
12	chr10:44357000-44361000	Enhancers	Muscle Satellite Cultured Cells	--
13	chr10:44357000-44361000	Enhancers	HUVEC	blood vessel
14	chr10:44357200-44360000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr10:44357200-44360000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr10:44357200-44360000	Enhancers	Osteobl	bone
17	chr10:44357200-44360400	Enhancers	NHLF	lung
18	chr10:44357200-44361000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr10:44357400-44359400	Enhancers	A549	lung
20	chr10:44357400-44359600	Enhancers	HepG2	liver
21	chr10:44357400-44359800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr10:44357400-44360000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:44357400-44360200	Enhancers	Hela-S3	cervix
24	chr10:44357400-44360400	Enhancers	NH-A	brain
25	chr10:44357400-44360600	Enhancers	Stomach Mucosa	stomach
26	chr10:44357600-44360000	Enhancers	Aorta	Aorta
27	chr10:44357600-44360200	Enhancers	HSMM	muscle
28	chr10:44357600-44360400	Enhancers	Fetal Intestine Small	intestine
29	chr10:44357600-44360600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr10:44357800-44358000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
31	chr10:44357800-44358000	Enhancers	HSMMtube	muscle
32	chr10:44357800-44358200	Enhancers	Fetal Kidney	kidney
33	chr10:44357800-44358400	Weak transcription	Duodenum Mucosa	Duodenum
34	chr10:44357800-44359200	Enhancers	Spleen	Spleen
35	chr10:44357800-44359800	Enhancers	Lung	lung
36	chr10:44357800-44360400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr10:44357800-44360600	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr10:44357800-44361600	Enhancers	Right Atrium	heart
39	chr10:44357800-44367200	Enhancers	Left Ventricle	heart

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