Variant report

Variant	rs17711565
Chromosome Location	chr19:18407643-18407644
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr19:18383365..18408325-chr19:18518460..18533256,66	K562	blood:
2	chr19:18399345..18407720-chr19:18430417..18436364,18	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-PGPEP1-4	chr19:18407534-18407915	NONHSAT062957

Variant related genes	Relation type
ENSG00000130511	Chromatin interaction
ENSG00000221167	Chromatin interaction
ENSG00000130520	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1079165	0.81[ASN][1000 genomes]
rs1079166	0.86[CHB][hapmap]
rs10854164	0.81[ASN][1000 genomes]
rs12461701	0.86[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs12461751	0.81[ASN][1000 genomes]
rs12463315	0.81[AMR][1000 genomes]
rs1421720	0.87[ASN][1000 genomes]
rs1549143	0.95[CHB][hapmap];0.95[JPT][hapmap];0.90[ASN][1000 genomes]
rs41347350	0.81[ASN][1000 genomes]
rs41481544	0.82[ASN][1000 genomes]
rs4808125	0.82[ASN][1000 genomes]
rs4808778	0.81[ASN][1000 genomes]
rs57090641	0.81[ASN][1000 genomes]
rs59961449	0.88[ASN][1000 genomes]
rs60086589	0.92[ASN][1000 genomes]
rs60170051	0.81[ASN][1000 genomes]
rs62120437	0.81[ASN][1000 genomes]
rs7247237	0.82[ASN][1000 genomes]
rs7247767	0.84[ASN][1000 genomes]
rs7248070	0.87[ASN][1000 genomes]
rs8103549	0.88[ASN][1000 genomes]
rs8108675	1.00[CHB][hapmap];0.89[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs8108909	0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532614	chr19:18033043-18573963	Flanking Active TSS Enhancers Active TSS Genic enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	204 gene(s)	inside rSNPs	diseases
2	nsv911251	chr19:18224729-18422364	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
3	nsv911253	chr19:18240127-18418044	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	136 gene(s)	inside rSNPs	diseases
4	nsv916325	chr19:18244780-18534927	Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	167 gene(s)	inside rSNPs	diseases
5	esv3323899	chr19:18343484-18620429	Enhancers Weak transcription Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	162 gene(s)	inside rSNPs	diseases
6	nsv911269	chr19:18351674-18418044	Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
7	nsv911270	chr19:18351674-18422364	Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	120 gene(s)	inside rSNPs	diseases
8	nsv911271	chr19:18362940-18453124	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
9	esv1833305	chr19:18378219-18408222	Active TSS Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	117 gene(s)	inside rSNPs	diseases
10	nsv911272	chr19:18378219-18439383	Flanking Active TSS Genic enhancers Weak transcription Enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	135 gene(s)	inside rSNPs	diseases
11	nsv911273	chr19:18386798-18454825	Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	134 gene(s)	inside rSNPs	diseases
12	esv3442194	chr19:18403852-18408550	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS	Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
13	esv3450606	chr19:18404552-18408250	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats	Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs17711565	FAM129C	cis	parietal	SCAN
rs17711565	NDUFA13	cis	parietal	SCAN
rs17711565	KIAA1683	cis	multi-tissue	Pritchard
rs17711565	KIAA1683	cis	cerebellum	SCAN
rs17711565	CHRM4	trans	multi-tissue	Pritchard
rs17711565	KIAA1683	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr19:18403600-18411600	Weak transcription	HSMMtube	muscle
2	chr19:18404400-18408200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr19:18404400-18409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
4	chr19:18404400-18411600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr19:18404400-18411600	Weak transcription	Left Ventricle	heart
6	chr19:18404400-18411600	Weak transcription	Right Ventricle	heart
7	chr19:18404400-18411800	Weak transcription	Duodenum Mucosa	Duodenum
8	chr19:18404400-18411800	Weak transcription	HSMM	muscle
9	chr19:18404400-18411800	Weak transcription	HUVEC	blood vessel
10	chr19:18404400-18414200	Weak transcription	Fetal Lung	lung
11	chr19:18404600-18409200	Weak transcription	Muscle Satellite Cultured Cells	--
12	chr19:18404600-18409400	Weak transcription	NHLF	lung
13	chr19:18404600-18411600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr19:18404600-18411600	Weak transcription	Fetal Muscle Leg	muscle
15	chr19:18404600-18411600	Weak transcription	NHDF-Ad	bronchial
16	chr19:18404600-18411800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr19:18404600-18411800	Weak transcription	Fetal Heart	heart
18	chr19:18404600-18411800	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr19:18404600-18414200	Weak transcription	Colon Smooth Muscle	Colon
20	chr19:18405000-18408200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr19:18405000-18409400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
22	chr19:18405000-18414200	Weak transcription	Fetal Stomach	stomach
23	chr19:18405200-18408200	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr19:18405200-18411600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr19:18405200-18411800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr19:18405400-18408000	Weak transcription	A549	lung
27	chr19:18405400-18408200	Weak transcription	Hela-S3	cervix
28	chr19:18405400-18409400	Weak transcription	NH-A	brain
29	chr19:18405400-18409600	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr19:18405400-18409800	Weak transcription	Rectal Mucosa Donor 31	rectum
31	chr19:18405400-18411400	Weak transcription	Skeletal Muscle Male	skeletal muscle
32	chr19:18405400-18411600	Weak transcription	Fetal Muscle Trunk	muscle
33	chr19:18405400-18412000	Weak transcription	Right Atrium	heart
34	chr19:18405400-18414200	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr19:18405400-18414400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr19:18405400-18414400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
37	chr19:18405400-18414800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr19:18405400-18415000	Weak transcription	H9 Cell Line	embryonic stem cell
39	chr19:18405600-18408200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
40	chr19:18405600-18409600	Weak transcription	Fetal Thymus	thymus
41	chr19:18405600-18409800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
42	chr19:18405800-18408200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr19:18405800-18408200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr19:18405800-18411800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr19:18405800-18412000	Weak transcription	Placenta Amnion	Placenta Amnion
46	chr19:18405800-18414200	Weak transcription	HUES6 Cell Line	embryonic stem cell
47	chr19:18405800-18414200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr19:18406000-18411400	Weak transcription	Placenta	Placenta
49	chr19:18406000-18412600	Weak transcription	Primary T helper cells fromperipheralblood	blood
50	chr19:18406000-18413800	Weak transcription	Fetal Intestine Small	intestine

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