Variant report

Variant	rs12048543
Chromosome Location	chr1:92050356-92050357
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	chr1:92049054..92051542-chr1:92061265..92062961,2	K562	blood:
2	chr1:92049157..92050899-chr1:92056086..92058376,2	K562	blood:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10458506	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10493854	0.96[ASN][1000 genomes]
rs10874794	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10874796	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11164971	0.89[ASN][1000 genomes]
rs11164978	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165002	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165008	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11165013	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12059556	0.96[ASN][1000 genomes]
rs12117800	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17503335	0.80[CHB][hapmap];0.81[ASN][1000 genomes]
rs1848435	0.89[ASN][1000 genomes]
rs4658235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4658236	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6604044	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6604045	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677520	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681573	0.96[ASN][1000 genomes]
rs6681883	0.96[ASN][1000 genomes]
rs6686665	0.96[ASN][1000 genomes]
rs6688706	0.96[ASN][1000 genomes]
rs6691704	0.96[ASN][1000 genomes]
rs906633	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv949516	chr1:91644418-92109261	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
2	nsv1009560	chr1:91897078-92270781	Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12048543	RPAP2	cis	cerebellum	SCAN

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92036400-92051000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr1:92041800-92051200	Weak transcription	Fetal Brain Male	brain
3	chr1:92045400-92051400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr1:92046000-92055000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
5	chr1:92047200-92052000	Enhancers	Fetal Stomach	stomach
6	chr1:92047400-92050600	Enhancers	NHDF-Ad	bronchial
7	chr1:92047400-92050800	Enhancers	NHLF	lung
8	chr1:92047600-92050800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:92047600-92051000	Enhancers	Ovary	ovary
10	chr1:92048000-92051800	Enhancers	Colon Smooth Muscle	Colon
11	chr1:92048000-92052200	Enhancers	Stomach Smooth Muscle	stomach
12	chr1:92048200-92051000	Weak transcription	Aorta	Aorta
13	chr1:92048400-92050800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr1:92048400-92054200	Weak transcription	K562	blood
15	chr1:92048600-92050400	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr1:92049000-92050400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr1:92049000-92051000	Enhancers	Duodenum Smooth Muscle	Duodenum
18	chr1:92049200-92050600	Weak transcription	Fetal Lung	lung
19	chr1:92049400-92050400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:92049400-92050400	Weak transcription	Rectal Smooth Muscle	rectum
21	chr1:92049400-92050800	Weak transcription	Fetal Thymus	thymus
22	chr1:92049400-92051000	Weak transcription	Right Ventricle	heart
23	chr1:92049400-92056400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
24	chr1:92049600-92061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr1:92050000-92050600	Flanking Active TSS	Fetal Heart	heart
26	chr1:92050000-92050800	Enhancers	Pancreatic Islets	Pancreatic Islet
27	chr1:92050000-92051000	Weak transcription	Right Atrium	heart
28	chr1:92050000-92051600	Enhancers	Fetal Kidney	kidney
29	chr1:92050200-92050400	Enhancers	Adipose Nuclei	Adipose
30	chr1:92050200-92051000	Weak transcription	Left Ventricle	heart
31	chr1:92050200-92051000	Weak transcription	Lung	lung

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