Variant report

Variant	rs6425648
Chromosome Location	chr1:180582355-180582356
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:180578916..180585462-chr1:180598253..180604360,12	K562	blood:
2	chr1:180579138..180584486-chr1:180589847..180594311,7	K562	blood:
3	chr1:180560325..180562003-chr1:180580501..180583189,2	K562	blood:
4	chr1:180568988..180574820-chr1:180577415..180583388,9	K562	blood:
5	chr1:180582342..180585190-chr1:180594710..180596635,2	K562	blood:
6	chr1:180581736..180587616-chr1:180588288..180595360,13	K562	blood:

Variant related genes	Relation type
ENSG00000143324	Chromatin interaction

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10157637	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10737349	1.00[CEU][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331546	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2331753	0.93[CEU][hapmap];1.00[MEX][hapmap];0.89[TSI][hapmap]
rs3903980	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3903981	0.93[CEU][hapmap];1.00[MEX][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3908502	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651074	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4651075	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4652524	0.93[CEU][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656378	0.92[CEU][hapmap];0.84[MEX][hapmap];0.89[TSI][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6664826	0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7548318	0.92[MEX][hapmap]

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	nsv1003359	chr1:180300936-180727561	Enhancers Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
2	nsv949311	chr1:180438895-180692815	ZNF genes & repeats Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
3	nsv872578	chr1:180510771-180842344	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs6425648	PAPPA2	cis	cerebellum	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:180578000-180587200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:180579400-180584200	Weak transcription	Fetal Brain Male	brain
3	chr1:180579800-180585200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
4	chr1:180580400-180585200	Weak transcription	Right Atrium	heart
5	chr1:180580400-180585600	Weak transcription	Right Ventricle	heart
6	chr1:180580400-180586600	Weak transcription	Lung	lung
7	chr1:180580600-180583600	Weak transcription	Esophagus	oesophagus
8	chr1:180580600-180583800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr1:180580600-180584000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr1:180580600-180585200	Weak transcription	Pancreas	Pancrea
11	chr1:180580600-180586600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr1:180580600-180587000	Weak transcription	Left Ventricle	heart
13	chr1:180580800-180583800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr1:180580800-180584000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr1:180580800-180584600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr1:180580800-180585600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
17	chr1:180581000-180583000	Weak transcription	HMEC	breast
18	chr1:180581000-180584600	Weak transcription	Stomach Mucosa	stomach
19	chr1:180581000-180585200	Weak transcription	NHLF	lung
20	chr1:180581000-180585600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr1:180581000-180585800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr1:180581000-180585800	Weak transcription	Cortex derived primary cultured neurospheres	brain
23	chr1:180581000-180586400	Weak transcription	Primary B cells from peripheral blood	blood
24	chr1:180581200-180583600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
25	chr1:180581400-180586400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr1:180581600-180582800	Weak transcription	NHEK	skin
27	chr1:180581600-180585400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
28	chr1:180581800-180584000	Weak transcription	Fetal Lung	lung
29	chr1:180581800-180600600	Weak transcription	Fetal Heart	heart
30	chr1:180582000-180583000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr1:180582000-180583000	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr1:180582000-180586600	Weak transcription	Primary monocytes fromperipheralblood	blood
33	chr1:180582000-180586600	Weak transcription	Monocytes-CD14+_RO01746	blood
34	chr1:180582200-180582600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
35	chr1:180582200-180582600	Weak transcription	K562	blood

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