Variant report

Variant	rs2670942
Chromosome Location	chr15:33604327-33604328
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTBP2	chr15:33602739-33604405	H1-hESC	embryonic stem cell:	n/a	n/a
2	POLR2A	chr15:33601555-33604941	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000259446	TF binding region

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs12148576	0.92[ASN][1000 genomes]
rs1567847	0.84[AMR][1000 genomes]
rs2670945	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2670946	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2670947	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2676071	0.92[ASN][1000 genomes]
rs2676072	0.80[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2676077	0.92[AFR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2676084	0.89[AFR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs907953	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv903982	chr15:33282844-33616150	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
2	nsv482299	chr15:33449137-33624122	Enhancers Weak transcription Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	nsv533346	chr15:33469439-33809641	Enhancers Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
4	nsv832963	chr15:33514798-33712442	Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2670942	RP11-489D6.2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:33601800-33604400	Active TSS	Brain Substantia Nigra	brain
2	chr15:33602000-33604400	Active TSS	Colon Smooth Muscle	Colon
3	chr15:33602000-33604600	Active TSS	Brain Angular Gyrus	brain
4	chr15:33602200-33604400	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
5	chr15:33602200-33604400	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
6	chr15:33602200-33604800	Bivalent/Poised TSS	iPS-15b Cell Line	embryonic stem cell
7	chr15:33602200-33608000	Active TSS	Brain Anterior Caudate	brain
8	chr15:33602400-33604400	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
9	chr15:33602400-33604400	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
10	chr15:33602400-33604400	Active TSS	Stomach Smooth Muscle	stomach
11	chr15:33602600-33604400	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
12	chr15:33602600-33604400	Bivalent/Poised TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr15:33602600-33604400	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
14	chr15:33602600-33604400	Bivalent/Poised TSS	Fetal Brain Female	brain
15	chr15:33603200-33604800	Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr15:33603400-33604400	Bivalent/Poised TSS	Skeletal Muscle Female	skeletal muscle
17	chr15:33603400-33605000	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
18	chr15:33603800-33604600	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
19	chr15:33604000-33604400	Bivalent Enhancer	Primary hematopoietic stem cells	blood
20	chr15:33604000-33604600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
21	chr15:33604000-33604600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr15:33604200-33604400	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
23	chr15:33604200-33604400	Bivalent/Poised TSS	Cortex derived primary cultured neurospheres	brain
24	chr15:33604200-33604400	Bivalent Enhancer	Brain Germinal Matrix	brain
25	chr15:33604200-33604400	Bivalent/Poised TSS	Fetal Muscle Trunk	muscle
26	chr15:33604200-33604400	Bivalent/Poised TSS	Fetal Stomach	stomach
27	chr15:33604200-33604400	Active TSS	Rectal Smooth Muscle	rectum
28	chr15:33604200-33604600	Bivalent Enhancer	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:33604200-33604600	Bivalent Enhancer	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:33604200-33604600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:33604200-33604800	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
32	chr15:33604200-33605200	Active TSS	Brain Inferior Temporal Lobe	brain

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