Variant report

Variant	rs13380277
Chromosome Location	chr15:51248837-51248838
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:51248351..51249869-chr15:51253170..51254880,2	MCF-7	breast:

Extended variants
information (count: 39 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs10152338	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11631696	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11635474	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963982	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16963985	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17521308	0.87[EUR][1000 genomes]
rs17521440	0.80[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600375	0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17600549	1.00[ASN][1000 genomes]
rs17600569	1.00[ASN][1000 genomes]
rs28552599	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57570932	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57603576	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58449611	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018161	0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018162	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018163	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs62018164	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018166	1.00[AFR][1000 genomes];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018184	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018215	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62018216	1.00[ASN][1000 genomes]
rs62018217	1.00[ASN][1000 genomes]
rs62018226	1.00[ASN][1000 genomes]
rs62020176	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020177	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020178	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9944192	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1047443	chr15:50744781-51647023	Strong transcription Active TSS Weak transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	82 gene(s)	inside rSNPs	diseases
2	nsv457136	chr15:50789125-51294995	Strong transcription ZNF genes & repeats Weak transcription Active TSS Enhancers Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
3	nsv569398	chr15:50789125-51294995	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
4	nsv569399	chr15:50874964-51562198	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Strong transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	70 gene(s)	inside rSNPs	diseases
5	nsv569400	chr15:50874964-51767265	ZNF genes & repeats Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers 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	80 gene(s)	inside rSNPs	diseases
6	nsv529339	chr15:51048579-51270372	Strong transcription Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
7	nsv428636	chr15:51154834-51298044	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	nsv569403	chr15:51191421-51304373	Enhancers Weak transcription Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers 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	20 gene(s)	inside rSNPs	diseases
9	nsv1038778	chr15:51196641-51356728	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	22 gene(s)	inside rSNPs	diseases
10	nsv904214	chr15:51204364-51535192	Strong transcription Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
11	nsv569404	chr15:51234595-51294995	ZNF genes & repeats Enhancers Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13380277	SPPL2A	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:51201800-51271600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:51205800-51249000	Weak transcription	Fetal Brain Male	brain
3	chr15:51205800-51254400	Weak transcription	Fetal Heart	heart
4	chr15:51208000-51250400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr15:51210600-51298400	Weak transcription	Stomach Mucosa	stomach
6	chr15:51232400-51250400	Weak transcription	HepG2	liver
7	chr15:51232800-51254000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr15:51233800-51254200	Strong transcription	Placenta	Placenta
9	chr15:51235200-51263800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr15:51237400-51249600	Weak transcription	Small Intestine	intestine
11	chr15:51239600-51253000	Strong transcription	Primary T cells from cord blood	blood
12	chr15:51240200-51251600	Strong transcription	Primary T helper cells PMA-I stimulated	--
13	chr15:51241000-51251600	Strong transcription	Primary T helper cells fromperipheralblood	blood
14	chr15:51241200-51252800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:51241400-51251800	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr15:51241800-51252400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr15:51241800-51253200	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
18	chr15:51241800-51253800	Strong transcription	Adipose Nuclei	Adipose
19	chr15:51242000-51249000	Strong transcription	Cortex derived primary cultured neurospheres	brain
20	chr15:51242000-51253400	Strong transcription	Liver	Liver
21	chr15:51242200-51249000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr15:51242200-51254800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
23	chr15:51242400-51249200	Strong transcription	Primary neutrophils fromperipheralblood	blood
24	chr15:51242600-51253200	Strong transcription	Duodenum Mucosa	Duodenum
25	chr15:51242600-51253200	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr15:51242800-51253200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
27	chr15:51242800-51258200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:51243000-51252400	Strong transcription	Primary T helper naive cells from peripheral blood	blood
29	chr15:51243400-51252600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
30	chr15:51243600-51250200	Weak transcription	Muscle Satellite Cultured Cells	--
31	chr15:51243600-51250400	Weak transcription	Colon Smooth Muscle	Colon
32	chr15:51243600-51250600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr15:51243600-51254400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr15:51243600-51256800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:51243600-51261400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:51243800-51250400	Weak transcription	NH-A	brain
37	chr15:51243800-51250600	Weak transcription	NHDF-Ad	bronchial
38	chr15:51243800-51250800	Weak transcription	Brain Substantia Nigra	brain
39	chr15:51243800-51251600	Weak transcription	Brain Angular Gyrus	brain
40	chr15:51243800-51283000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
41	chr15:51244400-51249600	Weak transcription	HUES6 Cell Line	embryonic stem cell
42	chr15:51244400-51250200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
43	chr15:51244600-51253600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr15:51244800-51249000	Strong transcription	Fetal Thymus	thymus
45	chr15:51245200-51249200	Strong transcription	Fetal Muscle Leg	muscle
46	chr15:51245400-51251600	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr15:51245400-51252000	Strong transcription	Fetal Muscle Trunk	muscle
48	chr15:51245600-51251800	Strong transcription	Left Ventricle	heart
49	chr15:51245600-51253800	Strong transcription	Brain Hippocampus Middle	brain
50	chr15:51245600-51255400	Strong transcription	HSMM	muscle

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