Variant report

Variant	rs1730452
Chromosome Location	chr12:47747697-47747698
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1345524	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.92[TSI][hapmap];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1620557	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642944	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642945	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642946	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642947	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1642948	0.85[CEU][hapmap];1.00[CHB][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1642949	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1730448	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730449	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1730454	0.90[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2078033	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141517	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2141518	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2936554	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2936555	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558785	chr12:47740440-48044011	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1730452	RPAP3	cis	parietal	SCAN

Chromatin state (count:26 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:47737400-47748400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr12:47744200-47749000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
3	chr12:47744600-47749200	Weak transcription	Primary monocytes fromperipheralblood	blood
4	chr12:47744600-47749200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr12:47744600-47749600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr12:47744600-47749800	Weak transcription	Osteobl	bone
7	chr12:47744600-47753800	Weak transcription	Fetal Thymus	thymus
8	chr12:47744800-47749200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr12:47744800-47749200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr12:47744800-47749200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr12:47744800-47749600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr12:47744800-47749800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr12:47745000-47749200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
14	chr12:47746000-47747800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
15	chr12:47746400-47749000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
16	chr12:47746400-47750000	Weak transcription	Fetal Brain Male	brain
17	chr12:47746800-47749200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:47746800-47749400	Weak transcription	Primary T cells from cord blood	blood
19	chr12:47746800-47749400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
20	chr12:47746800-47749800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
21	chr12:47747000-47749800	Enhancers	Primary B cells from cord blood	blood
22	chr12:47747200-47747800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
23	chr12:47747400-47747800	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
24	chr12:47747600-47748000	Flanking Active TSS	Primary B cells from peripheral blood	blood
25	chr12:47747600-47749200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr12:47747600-47750400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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