Variant report

Variant	rs1318292
Chromosome Location	chr15:99690776-99690777
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99688236..99691160-chr15:99691994..99693833,2	MCF-7	breast:

Extended variants
information (count: 27 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs12915090	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1670221	0.82[ASN][1000 genomes]
rs1703767	0.82[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1703768	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2602021	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602029	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2623180	0.88[EUR][1000 genomes]
rs2623181	0.89[EUR][1000 genomes]
rs2623193	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[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
rs1318292	SYNM	cis	Adipose Subcutaneous	GTEx
rs1318292	RP11-6O2.4	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99665000-99714200	Weak transcription	NHEK	skin
2	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
3	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
4	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:99676200-99696200	Weak transcription	NH-A	brain
6	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
7	chr15:99676800-99694400	Weak transcription	HUVEC	blood vessel
8	chr15:99677600-99695200	Weak transcription	Hela-S3	cervix
9	chr15:99677800-99696200	Weak transcription	HMEC	breast
10	chr15:99678200-99696400	Weak transcription	Placenta	Placenta
11	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
12	chr15:99679800-99696200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr15:99679800-99696200	Weak transcription	Esophagus	oesophagus
14	chr15:99684200-99694400	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr15:99684400-99691200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
16	chr15:99684400-99693600	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:99684400-99694000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
18	chr15:99684400-99696200	Weak transcription	HepG2	liver
19	chr15:99684600-99691000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr15:99684600-99694000	Weak transcription	HUES48 Cell Line	embryonic stem cell
21	chr15:99684600-99694400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr15:99684600-99694400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:99684600-99694600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr15:99684600-99695600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:99684600-99695800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
26	chr15:99684600-99695800	Weak transcription	Osteobl	bone
27	chr15:99684600-99698800	Weak transcription	Aorta	Aorta
28	chr15:99684600-99706600	Weak transcription	Right Atrium	heart
29	chr15:99684800-99709200	Weak transcription	Colonic Mucosa	Colon
30	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr15:99685000-99693200	Weak transcription	Liver	Liver
32	chr15:99685000-99697800	Weak transcription	NHDF-Ad	bronchial
33	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr15:99685200-99693400	Strong transcription	Fetal Intestine Small	intestine
35	chr15:99685400-99691800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:99685400-99691800	Strong transcription	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:99685600-99691200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:99685800-99690800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:99685800-99693400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr15:99686200-99692600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
41	chr15:99686800-99692600	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
42	chr15:99687800-99691800	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr15:99687800-99692000	Strong transcription	Ovary	ovary
44	chr15:99688000-99692000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr15:99688000-99692000	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr15:99688000-99692400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:99688400-99693600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:99688600-99692200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:99688600-99697000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
50	chr15:99688800-99691400	Strong transcription	Adipose Nuclei	Adipose

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