Variant report

Variant	rs4942990
Chromosome Location	chr13:51888812-51888813
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr13:51885872..51888143-chr13:51888698..51890403,2	MCF-7	breast:

Extended variants
information (count: 7 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs4941696	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4942989	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4942991	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7996243	0.81[EUR][1000 genomes]
rs9535644	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs9535645	0.82[EUR][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	nsv832611	chr13:51766472-51938314	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4942990	INTS6	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:33 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:51853000-51889600	Weak transcription	Brain Angular Gyrus	brain
2	chr13:51867600-51910800	Weak transcription	Pancreas	Pancrea
3	chr13:51877000-51889200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr13:51877800-51890000	Weak transcription	Lung	lung
5	chr13:51879800-51889200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr13:51881600-51889400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr13:51881800-51889000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr13:51883400-51889000	Weak transcription	HUES6 Cell Line	embryonic stem cell
9	chr13:51883400-51889200	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr13:51885400-51889400	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr13:51885600-51889000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr13:51885600-51889000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr13:51885800-51889000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
14	chr13:51885800-51889000	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr13:51885800-51889600	Weak transcription	Brain Hippocampus Middle	brain
16	chr13:51886200-51889000	Weak transcription	HUES48 Cell Line	embryonic stem cell
17	chr13:51886400-51889000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
18	chr13:51886400-51889200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr13:51886600-51889400	Weak transcription	Brain Anterior Caudate	brain
20	chr13:51886600-51889400	Weak transcription	Brain Cingulate Gyrus	brain
21	chr13:51886600-51889600	Weak transcription	Cortex derived primary cultured neurospheres	brain
22	chr13:51886600-51889600	Weak transcription	Brain Substantia Nigra	brain
23	chr13:51886600-51890400	Weak transcription	H1 Cell Line	embryonic stem cell
24	chr13:51886800-51889000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr13:51887600-51889800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr13:51887800-51890000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr13:51888000-51889200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr13:51888200-51890000	Weak transcription	Left Ventricle	heart
29	chr13:51888400-51889200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr13:51888400-51889400	Weak transcription	Right Atrium	heart
31	chr13:51888800-51889400	Enhancers	Primary hematopoietic stem cells	blood
32	chr13:51888800-51890600	Enhancers	Fetal Muscle Leg	muscle
33	chr13:51888800-51892400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived

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