Variant report

Variant	rs17819466
Chromosome Location	chr9:117819436-117819437
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr9:117819241-117822911	U87	brain:	n/a	n/a
2	POLR2A	chr9:117819281-117820311	U87	brain:	n/a	n/a

Variant related genes	Relation type
TNC	TF binding region

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs10117421	1.00[CHB][hapmap];0.96[TSI][hapmap]
rs1330361	1.00[CHB][hapmap];0.81[GIH][hapmap];0.96[TSI][hapmap];0.80[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1537011	0.80[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241078	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241442	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17241477	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17819299	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2001357	1.00[ASN][1000 genomes]
rs2150101	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28393206	0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4549855	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578423	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578424	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578425	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62578426	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62578427	0.82[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv831696	chr9:117701582-117874150	Weak transcription Enhancers Strong transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv615250	chr9:117768021-118012841	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv916912	chr9:117770039-118014140	Flanking Active TSS Enhancers Strong transcription Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17819466	PAPPA	cis	cerebellum	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:117782400-117848200	Weak transcription	Brain Substantia Nigra	brain
2	chr9:117791600-117833200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr9:117799200-117819800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
4	chr9:117800800-117825000	Weak transcription	Fetal Muscle Leg	muscle
5	chr9:117800800-117825200	Weak transcription	Fetal Muscle Trunk	muscle
6	chr9:117801800-117820200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr9:117802200-117848200	Weak transcription	Spleen	Spleen
8	chr9:117803400-117820000	Weak transcription	Aorta	Aorta
9	chr9:117803400-117820600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr9:117803600-117820200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr9:117803600-117825400	Weak transcription	Fetal Kidney	kidney
12	chr9:117807400-117819600	Strong transcription	NHDF-Ad	bronchial
13	chr9:117807400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr9:117809000-117825400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr9:117809200-117821000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr9:117810600-117825000	Weak transcription	Rectal Smooth Muscle	rectum
17	chr9:117812800-117825800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr9:117812800-117830600	Weak transcription	Fetal Lung	lung
19	chr9:117813200-117825000	Weak transcription	HUES6 Cell Line	embryonic stem cell
20	chr9:117815200-117821000	Strong transcription	Cortex derived primary cultured neurospheres	brain
21	chr9:117815200-117825200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
22	chr9:117815400-117859200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
23	chr9:117816000-117825200	Weak transcription	Esophagus	oesophagus
24	chr9:117816600-117820600	Strong transcription	Colon Smooth Muscle	Colon
25	chr9:117816800-117825000	Strong transcription	Stomach Smooth Muscle	stomach
26	chr9:117817000-117820400	Weak transcription	HSMM	muscle
27	chr9:117817400-117819800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
28	chr9:117817400-117820400	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr9:117817600-117819600	Strong transcription	Osteobl	bone
30	chr9:117817600-117819800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
31	chr9:117817600-117820200	Strong transcription	Fetal Stomach	stomach
32	chr9:117817800-117820200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr9:117817800-117820200	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
34	chr9:117817800-117850600	Weak transcription	Placenta Amnion	Placenta Amnion
35	chr9:117818000-117819800	Strong transcription	NH-A	brain
36	chr9:117818800-117819600	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
37	chr9:117818800-117823200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
38	chr9:117819200-117820200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr9:117819200-117820200	Strong transcription	NHLF	lung
40	chr9:117819200-117821000	Enhancers	HMEC	breast
41	chr9:117819200-117822400	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr9:117819200-117822600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr9:117819200-117827400	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
44	chr9:117819400-117819600	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
45	chr9:117819400-117820400	Genic enhancers	NHEK	skin
46	chr9:117819400-117825800	Weak transcription	Duodenum Smooth Muscle	Duodenum

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links