Variant report

Variant	rs579342
Chromosome Location	chr10:97229762-97229763
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	chr10:97220624..97225860-chr10:97227541..97231131,6	K562	blood:

Extended variants
information (count: 12 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1093082	0.84[AMR][1000 genomes]
rs1093083	0.84[AMR][1000 genomes]
rs12767115	1.00[JPT][hapmap]
rs1536447	0.82[GIH][hapmap]
rs1571132	0.87[GIH][hapmap]
rs17456435	1.00[JPT][hapmap]
rs4244315	1.00[CHB][hapmap];0.87[GIH][hapmap]
rs498671	1.00[ASN][1000 genomes]
rs499441	1.00[ASN][1000 genomes]
rs504385	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs512766	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045002	chr10:97214418-97250630	Weak transcription Enhancers Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs579342	LCOR	cis	parietal	SCAN
rs579342	NOC3L	cis	cerebellum	SCAN
rs579342	ARHGAP19	cis	parietal	SCAN
rs579342	CRTAC1	cis	cerebellum	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97213200-97234200	Weak transcription	Colonic Mucosa	Colon
2	chr10:97220600-97232000	Enhancers	Fetal Heart	heart
3	chr10:97223200-97230200	Enhancers	Fetal Brain Male	brain
4	chr10:97223200-97234000	Weak transcription	Ovary	ovary
5	chr10:97224800-97237000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr10:97226200-97230200	Enhancers	Breast Myoepithelial Primary Cells	Breast
7	chr10:97226200-97236000	Enhancers	HepG2	liver
8	chr10:97226400-97230400	Enhancers	HUES64 Cell Line	embryonic stem cell
9	chr10:97226400-97230600	Enhancers	Fetal Intestine Large	intestine
10	chr10:97226400-97232200	Enhancers	HUES6 Cell Line	embryonic stem cell
11	chr10:97226400-97232200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr10:97226400-97232200	Enhancers	Colon Smooth Muscle	Colon
13	chr10:97226400-97232400	Enhancers	Rectal Smooth Muscle	rectum
14	chr10:97226400-97236800	Enhancers	Skeletal Muscle Male	skeletal muscle
15	chr10:97226400-97242600	Enhancers	Fetal Intestine Small	intestine
16	chr10:97226600-97230400	Enhancers	iPS-20b Cell Line	embryonic stem cell
17	chr10:97226800-97230400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr10:97226800-97230400	Enhancers	Fetal Brain Female	brain
19	chr10:97226800-97234600	Enhancers	Skeletal Muscle Female	skeletal muscle
20	chr10:97227000-97229800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
21	chr10:97227000-97230400	Enhancers	Fetal Muscle Leg	muscle
22	chr10:97227000-97230400	Enhancers	Psoas Muscle	Psoas
23	chr10:97227400-97231400	Weak transcription	Stomach Mucosa	stomach
24	chr10:97227400-97231400	Weak transcription	HSMMtube	muscle
25	chr10:97227400-97233000	Weak transcription	Duodenum Mucosa	Duodenum
26	chr10:97227400-97233200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr10:97227400-97233400	Weak transcription	Fetal Lung	lung
28	chr10:97227400-97240400	Weak transcription	Spleen	Spleen
29	chr10:97227600-97229800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr10:97227600-97235800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr10:97228000-97230400	Enhancers	H1 Cell Line	embryonic stem cell
32	chr10:97228000-97230400	Enhancers	Brain Inferior Temporal Lobe	brain
33	chr10:97228200-97229800	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr10:97228200-97230400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr10:97228200-97230400	Enhancers	Liver	Liver
36	chr10:97228400-97230200	Weak transcription	Fetal Stomach	stomach
37	chr10:97228400-97230400	Enhancers	iPS-18 Cell Line	embryonic stem cell
38	chr10:97228400-97230600	Enhancers	Brain Anterior Caudate	brain
39	chr10:97228600-97233800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr10:97228600-97236800	Weak transcription	Fetal Muscle Trunk	muscle
41	chr10:97228800-97230600	Enhancers	HUES48 Cell Line	embryonic stem cell
42	chr10:97228800-97230600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
43	chr10:97229000-97229800	Enhancers	Rectal Mucosa Donor 29	rectum
44	chr10:97229000-97231200	Enhancers	ES-I3 Cell Line	embryonic stem cell
45	chr10:97229000-97235800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
46	chr10:97229200-97230200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
47	chr10:97229200-97230200	Enhancers	Brain Substantia Nigra	brain
48	chr10:97229200-97230400	Enhancers	H9 Cell Line	embryonic stem cell
49	chr10:97229200-97230400	Enhancers	Cortex derived primary cultured neurospheres	brain
50	chr10:97229200-97230400	Enhancers	Right Atrium	heart

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