Variant report

Variant	rs2602025
Chromosome Location	chr15:99697491-99697492
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	chr15:99697354..99699660-chr15:99705124..99708746,3	K562	blood:
2	chr15:99694775..99697545-chr15:99701020..99702847,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGPEP1L-3	chr15:99697436-99701345	ENSG00000259921.1

Variant related genes	Relation type
ENSG00000259921	Chromatin interaction
ENSG00000103852	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10902539	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1670213	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1670216	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1670224	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1670230	0.82[ASN][1000 genomes]
rs1703762	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703763	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703766	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1703771	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs187755	0.82[EUR][1000 genomes]
rs260114	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2602015	0.85[ASN][1000 genomes]
rs2602016	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2602018	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602020	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2602022	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2602026	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2602031	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2602035	0.82[AMR][1000 genomes]
rs2602038	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2623185	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2623188	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2623189	0.90[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs2623190	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2623191	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2924346	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs4573918	0.85[ASN][1000 genomes]
rs4965217	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6598224	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7163625	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs925236	0.83[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	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
5	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
6	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
7	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
8	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
9	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
10	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
11	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
12	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
13	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
14	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
15	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
16	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
17	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
18	nsv904546	chr15:99696046-100166300	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Strong transcription Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2602025	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	chr15:99676200-99703400	Weak transcription	GM12878-XiMat	blood
5	chr15:99678200-99708800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
6	chr15:99684600-99698800	Weak transcription	Aorta	Aorta
7	chr15:99684600-99706600	Weak transcription	Right Atrium	heart
8	chr15:99684800-99709200	Weak transcription	Colonic Mucosa	Colon
9	chr15:99684800-99721600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:99685000-99697800	Weak transcription	NHDF-Ad	bronchial
11	chr15:99685000-99720200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr15:99689400-99699800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:99689600-99699000	Weak transcription	Dnd41	blood
14	chr15:99689600-99707600	Weak transcription	Brain Hippocampus Middle	brain
15	chr15:99689600-99709600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr15:99689800-99697800	Weak transcription	Duodenum Smooth Muscle	Duodenum
17	chr15:99689800-99699400	Weak transcription	Brain Substantia Nigra	brain
18	chr15:99689800-99703400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr15:99689800-99709400	Weak transcription	Brain Angular Gyrus	brain
20	chr15:99690000-99708200	Weak transcription	Right Ventricle	heart
21	chr15:99690000-99709400	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr15:99690200-99697800	Weak transcription	Colon Smooth Muscle	Colon
23	chr15:99690200-99699000	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr15:99690200-99699000	Weak transcription	A549	lung
25	chr15:99690200-99704800	Weak transcription	Rectal Smooth Muscle	rectum
26	chr15:99690400-99705400	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr15:99690400-99706600	Weak transcription	Spleen	Spleen
28	chr15:99690400-99707400	Weak transcription	Gastric	stomach
29	chr15:99690400-99709800	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:99690600-99709000	Weak transcription	Fetal Heart	heart
31	chr15:99691600-99698200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr15:99691800-99698600	Weak transcription	Rectal Mucosa Donor 29	rectum
33	chr15:99691800-99699000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:99692000-99698200	Weak transcription	Fetal Intestine Large	intestine
35	chr15:99692000-99698600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
36	chr15:99692000-99707200	Weak transcription	HSMMtube	muscle
37	chr15:99692000-99717000	Weak transcription	HSMM	muscle
38	chr15:99692400-99698400	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:99692400-99698800	Weak transcription	Pancreas	Pancrea
40	chr15:99692400-99699200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr15:99692600-99698800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
42	chr15:99693000-99700600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr15:99693400-99698400	Weak transcription	Left Ventricle	heart
44	chr15:99693400-99698800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
45	chr15:99694800-99698200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
46	chr15:99694800-99698800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
47	chr15:99694800-99699200	Weak transcription	Fetal Lung	lung
48	chr15:99694800-99699400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
49	chr15:99694800-99702800	Weak transcription	HUVEC	blood vessel
50	chr15:99694800-99711000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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