Variant report

Variant	rs1719231
Chromosome Location	chr15:45571398-45571399
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:45570698..45571654-chr20:30134901..30135595,2	NB4	blood:
2	chr15:45547330..45549104-chr15:45570394..45573078,2	MCF-7	breast:
3	chr15:45570708..45573284-chr15:45693152..45695793,2	MCF-7	breast:
4	chr15:45491756..45494677-chr15:45570318..45572091,2	MCF-7	breast:
5	chr15:45458064..45460777-chr15:45570184..45573179,2	MCF-7	breast:
6	chr15:45464381..45467214-chr15:45569783..45571800,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SHF-3	chr15:45571395-45571449	ENSG00000259520.1
2	lnc-SHF-3	chr15:45571395-45571425	ENSG00000259520.1

No data

Variant related genes	Relation type
ENSG00000171763	Chromatin interaction
ENSG00000259539	Chromatin interaction
ENSG00000101898	Chromatin interaction
ENSG00000259520	Chromatin interaction
ENSG00000101294	Chromatin interaction
ENSG00000138606	Chromatin interaction
ENSG00000260035	Chromatin interaction
ENSG00000171766	Chromatin interaction

Extended variants
information (count: 76 )
Associated
traits (count: 15 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs1049508	0.85[CEU][hapmap]
rs1049518	1.00[CHB][hapmap]
rs10519018	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10519022	0.85[CEU][hapmap]
rs1060896	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1145076	1.00[CHB][hapmap]
rs1145077	1.00[CHB][hapmap]
rs1145086	1.00[CHB][hapmap]
rs1145089	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1145091	0.85[CEU][hapmap]
rs1145093	1.00[CHB][hapmap]
rs1153858	0.85[CEU][hapmap]
rs11632752	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11632778	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11632920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637838	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11637920	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11639420	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs11855527	0.85[EUR][1000 genomes]
rs12437840	0.85[CEU][hapmap]
rs12437887	0.85[CEU][hapmap]
rs12440038	0.85[CEU][hapmap]
rs12901747	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12904150	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12908818	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12910143	0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12911186	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12913645	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12915314	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1346266	0.85[CEU][hapmap]
rs1346267	1.00[CHB][hapmap]
rs1346268	0.85[CEU][hapmap]
rs1365610	0.85[CEU][hapmap]
rs1554521	0.85[CEU][hapmap]
rs1617984	1.00[CHB][hapmap]
rs1706770	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs1706772	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1706824	0.93[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719237	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1719250	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17536527	1.00[CHB][hapmap]
rs1820518	0.85[CEU][hapmap]
rs2413768	1.00[CHB][hapmap]
rs2413769	1.00[CEU][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2413772	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2413774	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2461705	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2467858	0.80[CEU][hapmap]
rs2486274	1.00[CHB][hapmap]
rs2687512	0.89[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3759899	0.85[CEU][hapmap]
rs3809472	0.85[CEU][hapmap]
rs4395020	0.85[CEU][hapmap]
rs4627277	0.86[CEU][hapmap]
rs4774580	0.85[CEU][hapmap]
rs4775911	0.85[CEU][hapmap]
rs6493143	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6493144	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6493145	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7164602	0.85[CEU][hapmap]
rs7165039	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7166580	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7167146	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs7171312	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8024620	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8033629	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8039138	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8039352	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8039354	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8039476	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8039540	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs872192	1.00[CHB][hapmap];1.00[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916374	chr15:45058112-45769052	Enhancers Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Weak transcription Bivalent Enhancer 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	104 gene(s)	inside rSNPs	diseases
2	nsv932147	chr15:45319178-45872076	Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	87 gene(s)	inside rSNPs	diseases
3	nsv869616	chr15:45401411-45736209	Active TSS Enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	76 gene(s)	inside rSNPs	diseases
4	nsv569315	chr15:45446156-45772448	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	75 gene(s)	inside rSNPs	diseases

mRNA abundance (count:15)

SNP	Gene	Cis/trans	Tissue	Source
rs1719231	SPATA5L1	cis	Thyroid	GTEx
rs1719231	CTD-2651B20.3	cis	Thyroid	GTEx
rs1719231	CTD-2651B20.3	cis	Muscle Skeletal	GTEx
rs1719231	CTD-2651B20.3	cis	Nerve Tibial	GTEx
rs1719231	SPATA5L1	cis	Esophagus Muscularis	GTEx
rs1719231	SPATA5L1	cis	Whole Blood	GTEx
rs1719231	CTD-2651B20.3	cis	Adipose Subcutaneous	GTEx
rs1719231	CTD-2651B20.4	cis	Nerve Tibial	GTEx
rs1719231	SPATA5L1	cis	Frontal Cortex	GTEx
rs1719231	CTD-2651B20.3	cis	Heart Left Ventricle	GTEx
rs1719231	CTD-2651B20.3	cis	Artery Tibial	GTEx
rs1719231	CTD-2651B20.3	cis	Esophagus Muscularis	GTEx
rs1719231	CTD-2651B20.3	cis	lung	GTEx
rs1719231	GATM	cis	Muscle Skeletal	GTEx
rs1719231	SPATA5L1	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45570200-45572000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr15:45570400-45572200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr15:45570400-45572200	Active TSS	iPS-15b Cell Line	embryonic stem cell
4	chr15:45570400-45572200	Active TSS	Psoas Muscle	Psoas
5	chr15:45570400-45572200	Active TSS	K562	blood
6	chr15:45570400-45572400	Active TSS	ES-I3 Cell Line	embryonic stem cell
7	chr15:45570400-45572400	Active TSS	H1 Cell Line	embryonic stem cell
8	chr15:45570400-45572400	Active TSS	iPS-20b Cell Line	embryonic stem cell
9	chr15:45570400-45572400	Flanking Active TSS	Adipose Nuclei	Adipose
10	chr15:45570400-45572400	Active TSS	HSMM	muscle
11	chr15:45570400-45572400	Active TSS	NHDF-Ad	bronchial
12	chr15:45570600-45571400	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
13	chr15:45570600-45571800	Active TSS	Fetal Muscle Trunk	muscle
14	chr15:45570600-45572000	Active TSS	ES-WA7 Cell Line	embryonic stem cell
15	chr15:45570600-45572000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr15:45570600-45572000	Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
17	chr15:45570600-45572000	Active TSS	Esophagus	oesophagus
18	chr15:45570600-45572000	Active TSS	Left Ventricle	heart
19	chr15:45570600-45572000	Active TSS	Rectal Smooth Muscle	rectum
20	chr15:45570600-45572200	Active TSS	H9 Cell Line	embryonic stem cell
21	chr15:45570600-45572200	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr15:45570600-45572200	Active TSS	HUES64 Cell Line	embryonic stem cell
23	chr15:45570600-45572200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
24	chr15:45570600-45572200	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
25	chr15:45570600-45572200	Active TSS	Pancreatic Islets	Pancreatic Islet
26	chr15:45570600-45572200	Active TSS	Right Atrium	heart
27	chr15:45570600-45572200	Active TSS	Right Ventricle	heart
28	chr15:45570600-45572400	Active TSS	HUES48 Cell Line	embryonic stem cell
29	chr15:45570600-45572400	Active TSS	HUES6 Cell Line	embryonic stem cell
30	chr15:45570600-45572400	Active TSS	iPS-18 Cell Line	embryonic stem cell
31	chr15:45570600-45572400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
32	chr15:45570600-45572400	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:45570600-45572400	Active TSS	HSMMtube	muscle
34	chr15:45570800-45571400	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
35	chr15:45570800-45571400	Flanking Active TSS	HUVEC	blood vessel
36	chr15:45570800-45571800	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:45570800-45571800	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr15:45570800-45571800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
39	chr15:45570800-45571800	Active TSS	Fetal Kidney	kidney
40	chr15:45570800-45572000	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
41	chr15:45570800-45572000	Active TSS	iPS DF 19.11 Cell Line	embryonic stem cell
42	chr15:45570800-45572000	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:45570800-45572000	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr15:45570800-45572000	Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:45570800-45572000	Active TSS	Aorta	Aorta
46	chr15:45570800-45572000	Active TSS	Colon Smooth Muscle	Colon
47	chr15:45570800-45572000	Active TSS	Pancreas	Pancrea
48	chr15:45570800-45572000	Active TSS	NHLF	lung
49	chr15:45570800-45572200	Flanking Active TSS	Primary B cells from peripheral blood	blood
50	chr15:45570800-45572200	Active TSS	A549	lung

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