Variant report

Variant	rs10785507
Chromosome Location	chr12:44978054-44978055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1037435	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1037436	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs10736021	0.87[AFR][1000 genomes]
rs10785501	0.86[JPT][hapmap]
rs10785503	0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10785505	0.90[CHB][hapmap];0.95[JPT][hapmap];0.98[ASN][1000 genomes]
rs10785506	0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10785509	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs10785510	0.86[ASN][1000 genomes]
rs10785511	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs10880652	0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10880653	0.81[CHB][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.87[ASN][1000 genomes]
rs10880654	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1349621	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs1376997	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1377280	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1452256	0.93[ASW][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.98[MKK][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs1452257	0.95[CHB][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs1493748	0.89[JPT][hapmap]
rs1552860	0.90[JPT][hapmap]
rs1869253	0.95[CHB][hapmap];0.95[CHD][hapmap];0.85[JPT][hapmap];0.98[ASN][1000 genomes]
rs1901556	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs1908179	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4143007	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.99[ASN][1000 genomes]
rs4768555	0.83[CHD][hapmap];0.90[JPT][hapmap]
rs4768556	0.90[JPT][hapmap]
rs61930801	0.98[ASN][1000 genomes]
rs61930833	0.97[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs728065	0.95[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.95[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs7486016	0.99[ASN][1000 genomes]
rs7953156	0.90[JPT][hapmap]
rs7966066	0.95[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.99[ASN][1000 genomes]
rs7979765	0.96[ASN][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	nsv1049818	chr12:44486312-45133783	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv3378050	chr12:44963059-45264289	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	esv2762976	chr12:44969431-45000228	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	n/a

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10785507	PSG2	trans	cerebellum	SCAN

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:44940200-44999600	Weak transcription	Primary T helper cells fromperipheralblood	blood
2	chr12:44943400-44998600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
3	chr12:44966800-45000600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
4	chr12:44976000-44979200	Enhancers	H1 Cell Line	embryonic stem cell
5	chr12:44976400-44983600	Weak transcription	Brain Germinal Matrix	brain
6	chr12:44976600-44978400	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr12:44976800-44978200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr12:44976800-44978400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr12:44977000-44978200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:44977000-44978200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
11	chr12:44977000-44978400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr12:44977200-44978200	Weak transcription	HUES48 Cell Line	embryonic stem cell
13	chr12:44977200-44984400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr12:44977400-44988600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr12:44977400-44995200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
16	chr12:44977400-44998800	Weak transcription	Primary T cells fromperipheralblood	blood
17	chr12:44977600-44979000	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:44977800-44979000	Enhancers	HUES6 Cell Line	embryonic stem cell
19	chr12:44978000-44978800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr12:44978000-44979200	Enhancers	HUES64 Cell Line	embryonic stem cell

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