Variant report

Variant	rs6677520
Chromosome Location	chr1:92052231-92052232
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:92046311..92049077-chr1:92051859..92054355,2	K562	blood:
2	chr1:92040469..92042505-chr1:92051071..92052577,2	K562	blood:
3	chr1:92047577..92050180-chr1:92051854..92054355,2	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs10458506	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10493854	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs10874794	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10874796	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11164971	0.89[ASN][1000 genomes]
rs11164978	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11165002	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165008	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11165013	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12048543	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12059556	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs12117800	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17503335	0.80[CHB][hapmap];0.82[ASN][1000 genomes]
rs1848435	0.89[ASN][1000 genomes]
rs4658235	0.80[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4658236	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs56034708	0.81[ASN][1000 genomes]
rs6604044	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6604045	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6681573	0.82[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6681883	0.83[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6686665	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6688706	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6691704	0.81[AFR][1000 genomes];0.98[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
rs6677520	RPAP2	cis	cerebellum	SCAN

Chromatin state (count:32 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:92046000-92055000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
2	chr1:92048400-92054200	Weak transcription	K562	blood
3	chr1:92049400-92056400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
4	chr1:92049600-92061600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr1:92050800-92054200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr1:92051000-92055400	Weak transcription	Ovary	ovary
7	chr1:92051000-92056400	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr1:92051200-92054600	Weak transcription	Fetal Lung	lung
9	chr1:92051200-92056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
10	chr1:92051400-92053000	Enhancers	Monocytes-CD14+_RO01746	blood
11	chr1:92051400-92056600	Weak transcription	Primary T cells from cord blood	blood
12	chr1:92051600-92053600	Enhancers	Primary neutrophils fromperipheralblood	blood
13	chr1:92051600-92056000	Weak transcription	Fetal Thymus	thymus
14	chr1:92051600-92056400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr1:92051600-92056800	Weak transcription	Left Ventricle	heart
16	chr1:92051600-92058000	Weak transcription	Right Ventricle	heart
17	chr1:92051600-92060000	Weak transcription	Lung	lung
18	chr1:92051800-92055800	Weak transcription	Placenta	Placenta
19	chr1:92051800-92056800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:92051800-92058200	Weak transcription	Right Atrium	heart
21	chr1:92051800-92067600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr1:92052000-92054400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr1:92052000-92055000	Weak transcription	Fetal Stomach	stomach
24	chr1:92052000-92056000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr1:92052200-92055000	Weak transcription	Fetal Heart	heart
26	chr1:92052200-92055000	Weak transcription	Fetal Kidney	kidney
27	chr1:92052200-92056000	Weak transcription	Primary hematopoietic stem cells	blood
28	chr1:92052200-92056200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
29	chr1:92052200-92056400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
30	chr1:92052200-92056600	Weak transcription	Primary B cells from cord blood	blood
31	chr1:92052200-92056800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
32	chr1:92052200-92057000	Weak transcription	Stomach Smooth Muscle	stomach

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