Variant report

Variant	rs1706827
Chromosome Location	chr15:45495912-45495913
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	JUND	chr15:45495744-45495938	HepG2	liver:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45494024..45495941-chr15:45555811..45558017,2	MCF-7	breast:
2	chr15:45494998..45498237-chr15:45508390..45511192,3	K562	blood:
3	chr15:45453899..45457914-chr15:45495194..45498173,3	K562	blood:
4	chr15:45491434..45494359-chr15:45494448..45497644,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260035	TF binding region
SHF	TF binding region
ENSG00000259932	TF binding region
ENSG00000138606	Chromatin interaction
ENSG00000260035	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs1145089	1.00[JPT][hapmap]
rs1620253	0.84[CEU][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes]
rs1648304	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1648307	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes]
rs1648308	0.85[CEU][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes]
rs1648310	0.80[AMR][1000 genomes]
rs1648312	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1648317	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1648318	0.91[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1706808	0.84[CEU][hapmap];1.00[JPT][hapmap]
rs1706813	0.88[CEU][hapmap];1.00[JPT][hapmap]
rs1706817	0.83[AMR][1000 genomes]
rs1706820	0.85[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1706826	0.84[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1706829	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2162246	0.88[CEU][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.81[AMR][1000 genomes]
rs2292468	0.84[CEU][hapmap]
rs2458237	0.83[AMR][1000 genomes]
rs2467819	0.83[AMR][1000 genomes]
rs2467820	0.83[AMR][1000 genomes]
rs28851313	0.93[ASN][1000 genomes]
rs4775830	0.85[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6493143	1.00[JPT][hapmap]
rs7169193	0.84[CEU][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv904187	chr15:45438537-45507738	Enhancers Flanking Active TSS Strong transcription Bivalent/Poised TSS Weak transcription Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	33 gene(s)	inside rSNPs	diseases
5	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1706827	CTD-2651B20.3	cis	Artery Tibial	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45493400-45497000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr15:45493600-45496000	Enhancers	Primary monocytes fromperipheralblood	blood
3	chr15:45493600-45497000	Weak transcription	HSMMtube	muscle
4	chr15:45493600-45497200	Weak transcription	Fetal Muscle Leg	muscle
5	chr15:45493600-45508000	Weak transcription	Right Atrium	heart
6	chr15:45493800-45497000	Weak transcription	Stomach Mucosa	stomach
7	chr15:45494000-45496200	Enhancers	Liver	Liver
8	chr15:45494000-45497000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:45494000-45497000	Weak transcription	Fetal Intestine Small	intestine
10	chr15:45494000-45497200	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr15:45494000-45497200	Weak transcription	Brain Hippocampus Middle	brain
12	chr15:45494000-45497200	Weak transcription	Fetal Intestine Large	intestine
13	chr15:45494200-45496800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr15:45495000-45496000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr15:45495000-45496200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr15:45495200-45496400	Enhancers	Osteobl	bone
17	chr15:45495400-45496000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:45495400-45496000	Enhancers	Breast Myoepithelial Primary Cells	Breast
19	chr15:45495400-45496000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr15:45495400-45496000	Enhancers	Duodenum Mucosa	Duodenum
21	chr15:45495400-45496000	Enhancers	Left Ventricle	heart
22	chr15:45495400-45496000	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr15:45495400-45496400	Enhancers	Ovary	ovary
24	chr15:45495600-45496000	Enhancers	Adipose Nuclei	Adipose
25	chr15:45495600-45496000	Flanking Bivalent TSS/Enh	HepG2	liver

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