Variant report

Variant	rs12148261
Chromosome Location	chr15:40478577-40478578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs11070256	1.00[CHD][hapmap]
rs11853477	1.00[ASN][1000 genomes]
rs11858747	1.00[CEU][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1494533	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1680156	1.00[ASN][1000 genomes]
rs17668261	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.91[TSI][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17668415	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1801389	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3759843	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap];1.00[ASN][1000 genomes]
rs62019997	1.00[ASN][1000 genomes]
rs62020025	1.00[ASN][1000 genomes]
rs62020027	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020029	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020031	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62020050	1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6492939	1.00[CHB][hapmap]
rs7165187	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7171605	1.00[ASN][1000 genomes]
rs7173181	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7182070	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7183293	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs74011373	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8023415	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	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12148261	NLGN4X	trans	lymphoblastoid	seeQTL
rs12148261	RPUSD2	cis	cerebellum	SCAN

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40453800-40525000	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:40454000-40515200	Weak transcription	Placenta Amnion	Placenta Amnion
3	chr15:40454600-40502400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
4	chr15:40454800-40524200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
5	chr15:40455400-40530400	Weak transcription	Fetal Brain Female	brain
6	chr15:40455600-40518200	Strong transcription	HUES6 Cell Line	embryonic stem cell
7	chr15:40455600-40522200	Strong transcription	HUES48 Cell Line	embryonic stem cell
8	chr15:40455600-40530400	Weak transcription	Brain Germinal Matrix	brain
9	chr15:40456200-40524000	Strong transcription	HUES64 Cell Line	embryonic stem cell
10	chr15:40456200-40524000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
11	chr15:40461600-40486800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:40462800-40482200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr15:40463800-40478800	Weak transcription	Fetal Intestine Small	intestine
14	chr15:40463800-40481400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr15:40463800-40482000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:40463800-40482600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr15:40464000-40485000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr15:40464000-40490200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr15:40465000-40489600	Weak transcription	Fetal Intestine Large	intestine
20	chr15:40468400-40485800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr15:40469000-40482600	Weak transcription	NHDF-Ad	bronchial
22	chr15:40471400-40517600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr15:40471400-40524400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr15:40473200-40517800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:40473600-40478600	Strong transcription	K562	blood
26	chr15:40473600-40479000	Strong transcription	Hela-S3	cervix
27	chr15:40473600-40487400	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr15:40473600-40525200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr15:40473800-40479200	Strong transcription	HUVEC	blood vessel
30	chr15:40473800-40479400	Strong transcription	HepG2	liver
31	chr15:40474000-40479600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr15:40474200-40483000	Strong transcription	H9 Cell Line	embryonic stem cell
33	chr15:40474200-40485000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:40474400-40485400	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
35	chr15:40474600-40478600	Strong transcription	NHEK	skin
36	chr15:40474600-40478800	Strong transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:40474800-40482800	Strong transcription	Fetal Muscle Trunk	muscle
38	chr15:40475000-40491600	Weak transcription	Rectal Mucosa Donor 29	rectum
39	chr15:40475000-40526400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr15:40475200-40479400	Strong transcription	Monocytes-CD14+_RO01746	blood
41	chr15:40475400-40480000	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr15:40475400-40488800	Weak transcription	NH-A	brain
43	chr15:40475400-40522600	Strong transcription	Dnd41	blood
44	chr15:40475600-40490000	Strong transcription	Fetal Thymus	thymus
45	chr15:40475800-40483600	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:40476200-40481000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:40476200-40489400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
48	chr15:40476400-40479000	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr15:40476400-40483400	Strong transcription	Fetal Stomach	stomach
50	chr15:40476600-40490000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood

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