Variant report

Variant	rs17464560
Chromosome Location	chr10:44349516-44349517
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:44340953..44343939-chr10:44348201..44350447,2	MCF-7	breast:
2	chr10:44349396..44350216-chr10:44669102..44669618,2	MCF-7	breast:
3	chr10:44185207..44186112-chr10:44349223..44350193,2	MCF-7	breast:
4	chr10:44344766..44346782-chr10:44348316..44349899,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:40)

rs_ID	r²[population]
rs1008803	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1009769	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1009770	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1009771	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10899921	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs10899923	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10899925	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10899927	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10899928	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs10899929	0.92[EUR][1000 genomes]
rs10899932	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10899937	0.81[EUR][1000 genomes]
rs10899944	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10899945	0.82[EUR][1000 genomes]
rs11238736	0.81[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11238737	0.88[CHB][hapmap];1.00[JPT][hapmap];0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11238741	0.94[EUR][1000 genomes]
rs11238749	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11238750	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11238753	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11238754	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238756	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs11238759	0.89[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238761	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11238764	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12357341	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12359360	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1468061	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17465611	0.81[EUR][1000 genomes]
rs2031513	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2169200	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4948580	0.87[EUR][1000 genomes]
rs4948581	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4948786	0.92[CEU][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs56034709	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7903927	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7909314	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs881714	0.94[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs912805	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs9633744	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17464560	LINC00840	cis	lung	GTEx

Chromatin state (count:37 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:44340800-44357600	Weak transcription	Aorta	Aorta
2	chr10:44342200-44350200	Weak transcription	Right Atrium	heart
3	chr10:44343000-44352400	Weak transcription	HUVEC	blood vessel
4	chr10:44343600-44349600	Weak transcription	Left Ventricle	heart
5	chr10:44346600-44350800	Enhancers	Placenta	Placenta
6	chr10:44346600-44353000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr10:44347000-44350400	Enhancers	Breast Myoepithelial Primary Cells	Breast
8	chr10:44347200-44351800	Enhancers	Placenta Amnion	Placenta Amnion
9	chr10:44347400-44350200	Enhancers	HSMMtube	muscle
10	chr10:44348400-44352600	Weak transcription	Fetal Brain Female	brain
11	chr10:44348600-44350400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr10:44348600-44350800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
13	chr10:44348600-44351200	Weak transcription	Pancreas	Pancrea
14	chr10:44348600-44352600	Weak transcription	Fetal Brain Male	brain
15	chr10:44348800-44350200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr10:44349000-44350000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr10:44349000-44350200	Enhancers	Muscle Satellite Cultured Cells	--
18	chr10:44349200-44349600	Enhancers	HMEC	breast
19	chr10:44349200-44349600	Flanking Active TSS	NHDF-Ad	bronchial
20	chr10:44349200-44349800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr10:44349200-44349800	Enhancers	Fetal Muscle Leg	muscle
22	chr10:44349200-44350000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr10:44349200-44350000	Bivalent Enhancer	HepG2	liver
24	chr10:44349200-44350000	Enhancers	NHLF	lung
25	chr10:44349200-44350000	Enhancers	Osteobl	bone
26	chr10:44349200-44350200	Enhancers	HSMM	muscle
27	chr10:44349200-44350200	Enhancers	NHEK	skin
28	chr10:44349200-44350400	Enhancers	Hela-S3	cervix
29	chr10:44349200-44352000	Enhancers	Fetal Heart	heart
30	chr10:44349400-44349600	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr10:44349400-44349800	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr10:44349400-44350000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
33	chr10:44349400-44350000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
34	chr10:44349400-44350000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr10:44349400-44350200	Enhancers	Adipose Nuclei	Adipose
36	chr10:44349400-44350200	Bivalent Enhancer	NH-A	brain
37	chr10:44349400-44350400	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin

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