Variant report

Variant	rs9840370
Chromosome Location	chr3:100173525-100173526
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	chr3:100119733..100122215-chr3:100171040..100173850,2	K562	blood:

Variant related genes	Relation type
ENSG00000154174	Chromatin interaction
ENSG00000206535	Chromatin interaction

Extended variants
information (count: 10 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1132022	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712077	0.87[EUR][1000 genomes]
rs4928050	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4928071	0.89[EUR][1000 genomes]
rs4928073	0.89[ASN][1000 genomes]
rs6797397	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7434167	0.89[EUR][1000 genomes]
rs7434244	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9290059	0.89[EUR][1000 genomes]
rs9820973	0.86[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9840370	LNP1	cis	Muscle Skeletal	GTEx
rs9840370	TOMM70A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:100144200-100175600	Weak transcription	Psoas Muscle	Psoas
2	chr3:100146400-100177800	Weak transcription	Ovary	ovary
3	chr3:100148200-100182400	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr3:100158400-100176400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:100163000-100177200	Weak transcription	HepG2	liver
6	chr3:100163400-100176400	Weak transcription	Fetal Lung	lung
7	chr3:100166800-100173600	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr3:100168600-100176200	Weak transcription	Brain Angular Gyrus	brain
9	chr3:100168800-100174000	Weak transcription	HUES48 Cell Line	embryonic stem cell
10	chr3:100168800-100175600	Weak transcription	Brain Germinal Matrix	brain
11	chr3:100168800-100177800	Weak transcription	Left Ventricle	heart
12	chr3:100169400-100175600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr3:100169800-100174400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr3:100169800-100176400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr3:100170000-100174600	Weak transcription	Fetal Muscle Leg	muscle
16	chr3:100170200-100175000	Weak transcription	Fetal Brain Female	brain
17	chr3:100170600-100176400	Weak transcription	Brain Cingulate Gyrus	brain
18	chr3:100170600-100177400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
19	chr3:100170800-100175800	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr3:100170800-100175800	Weak transcription	Duodenum Smooth Muscle	Duodenum
21	chr3:100170800-100177400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
22	chr3:100172000-100176400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr3:100172200-100174200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:100172200-100185200	Weak transcription	Aorta	Aorta
25	chr3:100172400-100176200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
26	chr3:100172400-100177600	Weak transcription	Fetal Stomach	stomach
27	chr3:100173000-100177400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr3:100173200-100173600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr3:100173200-100174600	Enhancers	iPS-15b Cell Line	embryonic stem cell
30	chr3:100173200-100176000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr3:100173400-100173600	Flanking Active TSS	Liver	Liver
32	chr3:100173400-100174400	Enhancers	Fetal Heart	heart

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