Variant report

Variant	rs260118
Chromosome Location	chr15:99679830-99679831
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:99677279..99681777-chr15:99693510..99696751,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SYNM-2	chr15:99679522-99681244	ENSG00000261616.1

Variant related genes	Relation type
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs11247060	0.85[JPT][hapmap]
rs12903602	1.00[CHB][hapmap]
rs1670217	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1670220	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1670222	0.88[CEU][hapmap];0.92[YRI][hapmap]
rs1670223	0.88[CEU][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1670227	0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1703770	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs181987	0.85[JPT][hapmap]
rs260088	0.85[JPT][hapmap]
rs260089	0.85[JPT][hapmap]
rs260090	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs260115	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs260116	0.85[JPT][hapmap]
rs260117	0.85[JPT][hapmap]
rs2602014	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2602019	0.81[EUR][1000 genomes]
rs2602027	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2602028	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs2602033	1.00[CEU][hapmap]
rs2602037	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2602039	1.00[CHB][hapmap]
rs2623178	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs2623194	1.00[CHB][hapmap]
rs2623196	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2623197	0.88[CHB][hapmap]
rs4965447	0.85[JPT][hapmap]
rs7167599	0.86[JPT][hapmap]
rs755551	0.86[JPT][hapmap]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs260118	RP11-6O2.4	cis	Nerve Tibial	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:99664600-99682200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:99664800-99682000	Weak transcription	HUES64 Cell Line	embryonic stem cell
3	chr15:99664800-99688600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr15:99665000-99683800	Weak transcription	Rectal Mucosa Donor 31	rectum
5	chr15:99665000-99714200	Weak transcription	NHEK	skin
6	chr15:99665200-99687800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr15:99666000-99683000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr15:99666200-99680400	Weak transcription	Fetal Brain Female	brain
9	chr15:99666200-99684200	Weak transcription	HSMMtube	muscle
10	chr15:99670800-99680600	Weak transcription	Thymus	Thymus
11	chr15:99673200-99789400	Weak transcription	Small Intestine	intestine
12	chr15:99674400-99704200	Weak transcription	Fetal Kidney	kidney
13	chr15:99676000-99683200	Weak transcription	Stomach Mucosa	stomach
14	chr15:99676200-99682600	Weak transcription	NHDF-Ad	bronchial
15	chr15:99676200-99688800	Weak transcription	Brain Angular Gyrus	brain
16	chr15:99676200-99689000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
17	chr15:99676200-99691000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr15:99676200-99696200	Weak transcription	NH-A	brain
19	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
20	chr15:99676400-99680400	Strong transcription	Fetal Stomach	stomach
21	chr15:99676400-99688600	Weak transcription	Fetal Heart	heart
22	chr15:99676400-99690200	Weak transcription	HSMM	muscle
23	chr15:99676800-99694400	Weak transcription	HUVEC	blood vessel
24	chr15:99677000-99682400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
25	chr15:99677200-99680200	Enhancers	HUES6 Cell Line	embryonic stem cell
26	chr15:99677400-99682200	Weak transcription	Brain Substantia Nigra	brain
27	chr15:99677400-99682200	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:99677600-99681800	Weak transcription	Colon Smooth Muscle	Colon
29	chr15:99677600-99684000	Weak transcription	Colonic Mucosa	Colon
30	chr15:99677600-99695200	Weak transcription	Hela-S3	cervix
31	chr15:99677800-99683600	Weak transcription	Brain Hippocampus Middle	brain
32	chr15:99677800-99696200	Weak transcription	HMEC	breast
33	chr15:99678000-99683600	Weak transcription	Fetal Lung	lung
34	chr15:99678000-99683800	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
35	chr15:99678000-99683800	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr15:99678000-99683800	Weak transcription	Osteobl	bone
37	chr15:99678000-99687800	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:99678200-99689000	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:99678200-99696400	Weak transcription	Placenta	Placenta
40	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
41	chr15:99678400-99683000	Weak transcription	Liver	Liver
42	chr15:99678400-99689200	Weak transcription	Right Ventricle	heart
43	chr15:99678800-99680000	Enhancers	HUES48 Cell Line	embryonic stem cell
44	chr15:99679000-99684000	Weak transcription	Lung	lung
45	chr15:99679200-99680400	Enhancers	Breast Myoepithelial Primary Cells	Breast
46	chr15:99679200-99682200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr15:99679200-99682200	Weak transcription	Left Ventricle	heart
48	chr15:99679200-99682200	Weak transcription	Psoas Muscle	Psoas
49	chr15:99679200-99684000	Weak transcription	Sigmoid Colon	Sigmoid Colon
50	chr15:99679400-99680200	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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