Variant report

Variant	rs906759
Chromosome Location	chr15:99664646-99664647
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:99643707..99645442-chr15:99663437..99665092,2	MCF-7	breast:
2	chr15:99663432..99665582-chr15:99669095..99671723,2	MCF-7	breast:
3	chr15:99664100..99665791-chr15:99675684..99677549,2	MCF-7	breast:
4	chr15:99664166..99665904-chr15:99695053..99697897,2	MCF-7	breast:
5	chr15:99658366..99661719-chr15:99663030..99668142,6	MCF-7	breast:

Variant related genes	Relation type
ENSG00000182253	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs12148438	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12441651	0.85[AFR][1000 genomes]
rs12595457	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1670245	0.87[ASN][1000 genomes]
rs1670246	0.89[ASN][1000 genomes]
rs1703776	0.84[ASN][1000 genomes]
rs1703777	0.83[ASN][1000 genomes]
rs2663105	0.88[ASN][1000 genomes]
rs4965445	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7167303	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs896700	0.85[ASN][1000 genomes]
rs896701	0.86[ASN][1000 genomes]
rs906762	0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv531079	chr15:98907913-99878547	Strong transcription Weak transcription Genic enhancers Active TSS Enhancers ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	97 gene(s)	inside rSNPs	diseases
2	nsv1039575	chr15:98982045-99924685	Weak transcription Bivalent Enhancer Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
3	nsv869529	chr15:99416774-99903351	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
4	nsv533375	chr15:99443534-99696221	Enhancers Genic enhancers Bivalent/Poised TSS Weak transcription Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
5	nsv1050982	chr15:99450004-99725825	Enhancers Strong transcription Genic enhancers Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
6	nsv530685	chr15:99452377-99713365	Bivalent/Poised TSS Strong transcription Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases
7	nsv1055008	chr15:99477144-100019861	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
8	nsv1045124	chr15:99504843-99847210	Strong transcription Active TSS Weak transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
9	nsv1038870	chr15:99510479-99768374	Enhancers Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
10	nsv904543	chr15:99513231-99991506	Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
11	nsv533926	chr15:99519820-99997114	Enhancers Active TSS Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
12	nsv915926	chr15:99519820-100138705	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
13	nsv1051782	chr15:99621061-99792967	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
14	nsv916822	chr15:99621061-99878564	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
15	nsv949203	chr15:99621061-99932797	Strong transcription Weak transcription Enhancers Bivalent Enhancer Active TSS Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	31 gene(s)	inside rSNPs	diseases
16	nsv817289	chr15:99621061-100138705	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
17	nsv431411	chr15:99621061-100143999	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
18	nsv570716	chr15:99629901-99916332	Weak transcription Active TSS Transcr. at gene 5' and 3' Strong transcription Enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs906759	RP11-6O2.4	cis	Adipose Subcutaneous	GTEx
rs906759	SYNM	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99647600-99672400	Weak transcription	Esophagus	oesophagus
2	chr15:99652000-99669800	Weak transcription	Thymus	Thymus
3	chr15:99660600-99671600	Weak transcription	Liver	Liver
4	chr15:99661000-99666400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr15:99662600-99666600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr15:99662800-99665600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:99662800-99666200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr15:99663200-99665000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:99663200-99665000	Enhancers	Fetal Intestine Large	intestine
10	chr15:99663200-99665000	Enhancers	Rectal Mucosa Donor 31	rectum
11	chr15:99663200-99665200	Enhancers	ES-I3 Cell Line	embryonic stem cell
12	chr15:99663200-99665200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:99663200-99666200	Flanking Active TSS	Hela-S3	cervix
14	chr15:99663200-99666400	Enhancers	Fetal Brain Male	brain
15	chr15:99663200-99666400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
16	chr15:99663200-99666800	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr15:99663200-99666800	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
18	chr15:99663400-99664800	Enhancers	Fetal Lung	lung
19	chr15:99663400-99665000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr15:99663400-99665200	Enhancers	iPS-20b Cell Line	embryonic stem cell
21	chr15:99663400-99665800	Enhancers	Lung	lung
22	chr15:99663600-99664800	Enhancers	HUES64 Cell Line	embryonic stem cell
23	chr15:99663600-99664800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr15:99663600-99664800	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:99663600-99664800	Flanking Active TSS	Adipose Nuclei	Adipose
26	chr15:99663600-99664800	Flanking Active TSS	Brain Hippocampus Middle	brain
27	chr15:99663600-99664800	Enhancers	Fetal Thymus	thymus
28	chr15:99663600-99664800	Enhancers	Pancreas	Pancrea
29	chr15:99663600-99664800	Flanking Active TSS	NH-A	brain
30	chr15:99663600-99664800	Flanking Active TSS	Osteobl	bone
31	chr15:99663600-99665000	Enhancers	Primary monocytes fromperipheralblood	blood
32	chr15:99663600-99665000	Flanking Active TSS	HSMM	muscle
33	chr15:99663600-99665200	Enhancers	H1 Cell Line	embryonic stem cell
34	chr15:99663600-99665200	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr15:99663600-99665200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
36	chr15:99663600-99665200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
37	chr15:99663600-99665200	Enhancers	Placenta Amnion	Placenta Amnion
38	chr15:99663600-99665400	Enhancers	Placenta	Placenta
39	chr15:99663600-99665600	Enhancers	Gastric	stomach
40	chr15:99663600-99665800	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr15:99663600-99666000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
42	chr15:99663600-99667000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr15:99663600-99679400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
44	chr15:99663800-99664800	Enhancers	Primary hematopoietic stem cells	blood
45	chr15:99663800-99664800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
46	chr15:99663800-99665000	Genic enhancers	Fetal Intestine Small	intestine
47	chr15:99664000-99665000	Transcr. at gene 5' and 3'	Colon Smooth Muscle	Colon
48	chr15:99664000-99666000	Flanking Active TSS	HSMMtube	muscle
49	chr15:99664000-99666200	Enhancers	Fetal Brain Female	brain
50	chr15:99664200-99664800	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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