Variant report

Variant	rs4279875
Chromosome Location	chr1:57917398-57917399
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 70 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs10047071	0.86[JPT][hapmap]
rs10047073	0.86[JPT][hapmap]
rs10493219	0.86[JPT][hapmap]
rs10493225	1.00[CHB][hapmap];1.00[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs10889034	1.00[JPT][hapmap]
rs10889044	0.86[JPT][hapmap]
rs10889047	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11207010	1.00[JPT][hapmap]
rs11207011	1.00[JPT][hapmap]
rs11207027	0.82[CHB][hapmap]
rs1155680	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11584169	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11585751	0.86[JPT][hapmap]
rs12044871	0.81[CEU][hapmap];0.82[MEX][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12044874	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12044912	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12046102	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12061812	1.00[JPT][hapmap]
rs12087888	1.00[JPT][hapmap]
rs12121490	0.97[ASN][1000 genomes]
rs12128305	1.00[JPT][hapmap]
rs12132685	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12136107	0.86[JPT][hapmap]
rs12137169	0.86[JPT][hapmap]
rs12142821	1.00[JPT][hapmap]
rs12240237	0.86[JPT][hapmap]
rs1240442	0.86[JPT][hapmap]
rs12405761	0.86[JPT][hapmap]
rs12407896	0.85[CHB][hapmap]
rs12568449	1.00[JPT][hapmap]
rs12726704	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs12752978	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1334239	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1334240	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1357783	0.93[MEX][hapmap];0.84[TSI][hapmap];0.83[EUR][1000 genomes]
rs1424463	0.84[JPT][hapmap]
rs1424467	0.85[JPT][hapmap]
rs166514	1.00[JPT][hapmap]
rs17115686	0.86[JPT][hapmap]
rs17424216	0.86[JPT][hapmap]
rs17425017	0.86[JPT][hapmap]
rs17425189	1.00[JPT][hapmap]
rs17456661	1.00[JPT][hapmap]
rs17459384	0.86[JPT][hapmap]
rs17459948	0.82[ASW][hapmap];0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2216808	0.86[JPT][hapmap]
rs2405696	0.86[JPT][hapmap]
rs2405994	0.86[JPT][hapmap]
rs267638	1.00[JPT][hapmap]
rs267647	1.00[JPT][hapmap]
rs267650	1.00[JPT][hapmap]
rs2781325	1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2860532	1.00[YRI][hapmap]
rs34252256	0.91[ASN][1000 genomes]
rs390203	1.00[JPT][hapmap]
rs3909556	0.86[JPT][hapmap]
rs439378	1.00[JPT][hapmap]
rs4912163	1.00[JPT][hapmap]
rs4912244	0.86[JPT][hapmap]
rs59744820	0.88[ASN][1000 genomes]
rs6669975	1.00[JPT][hapmap]
rs736109	1.00[JPT][hapmap]
rs736110	1.00[JPT][hapmap]
rs746937	1.00[JPT][hapmap]
rs7513076	0.86[JPT][hapmap]
rs7535763	0.86[JPT][hapmap]
rs9436130	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.98[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[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	nsv817216	chr1:57801783-58130775	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv1001771	chr1:57837089-58068175	Bivalent/Poised TSS Weak transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv870908	chr1:57884310-58037783	Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs4279875	C8A	cis	cerebellum	SCAN
rs4279875	DAB1	cis	cerebellum	SCAN
rs4279875	TMEM59	cis	cerebellum	SCAN
rs4279875	LDLRAD1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:57915600-57917800	Enhancers	HUES48 Cell Line	embryonic stem cell
2	chr1:57915800-57917400	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr1:57916000-57917400	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:57916000-57917800	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
5	chr1:57916200-57917800	Enhancers	H1 Cell Line	embryonic stem cell
6	chr1:57916200-57917800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
7	chr1:57916400-57917400	Enhancers	ES-I3 Cell Line	embryonic stem cell
8	chr1:57916400-57917400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr1:57916400-57917400	Enhancers	HUES6 Cell Line	embryonic stem cell
10	chr1:57916400-57917400	Enhancers	iPS-20b Cell Line	embryonic stem cell
11	chr1:57916800-57917400	Enhancers	Fetal Intestine Large	intestine
12	chr1:57916800-57917600	Enhancers	ES-WA7 Cell Line	embryonic stem cell
13	chr1:57916800-57917600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived

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