Variant report

Variant	rs3820059
Chromosome Location	chr1:169391154-169391155
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:169390021..169391696-chr1:169393903..169395774,2	K562	blood:
2	chr1:169388927..169391330-chr1:169400055..169402370,2	MCF-7	breast:

Extended variants
information (count: 73 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:70)

rs_ID	r²[population]
rs10429893	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465575	0.81[AFR][1000 genomes];0.87[AMR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10465576	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10489189	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10732287	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs10737546	0.81[YRI][hapmap]
rs10753786	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10800424	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs10800425	1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap]
rs10800435	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.83[AMR][1000 genomes]
rs10800438	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800440	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10800441	0.85[CEU][hapmap]
rs10800447	0.81[YRI][hapmap]
rs10919120	0.88[CHD][hapmap]
rs10919124	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs10919132	0.82[ASW][hapmap];0.89[YRI][hapmap]
rs10919168	0.81[ASN][1000 genomes]
rs10919174	0.82[JPT][hapmap];0.82[AMR][1000 genomes]
rs1124843	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1133814	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12024897	0.85[CEU][hapmap]
rs12029566	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12076993	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1208134	0.81[ASN][1000 genomes]
rs1208135	0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs1208377	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.90[MKK][hapmap];0.81[YRI][hapmap]
rs12563090	0.85[CEU][hapmap]
rs1400836	1.00[ASW][hapmap];1.00[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];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1517744	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1517747	0.82[JPT][hapmap];0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs1591733	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.87[MKK][hapmap];0.85[YRI][hapmap]
rs1856303	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs1914505	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1980198	0.85[CEU][hapmap]
rs1983546	0.87[CHD][hapmap];0.82[JPT][hapmap]
rs2003653	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2037250	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs2138898	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2176473	0.81[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.93[MKK][hapmap];0.84[TSI][hapmap];0.89[YRI][hapmap];0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2275299	0.85[CEU][hapmap]
rs2300158	0.89[YRI][hapmap]
rs3766095	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs3818844	0.85[CEU][hapmap]
rs3905328	1.00[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];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4264046	1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap]
rs4656183	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656670	0.85[CEU][hapmap]
rs4656672	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6427185	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap]
rs6427187	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6656822	0.87[CHD][hapmap];0.82[JPT][hapmap];0.83[LWK][hapmap];0.82[AMR][1000 genomes]
rs6669741	0.85[CEU][hapmap]
rs6669901	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6672589	0.81[YRI][hapmap]
rs6677410	0.85[CEU][hapmap]
rs6696810	0.85[CEU][hapmap]
rs6700375	0.82[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7415756	0.89[CEU][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7521582	1.00[CHD][hapmap]
rs7533257	0.81[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.85[MKK][hapmap];0.85[YRI][hapmap]
rs7534737	0.85[CEU][hapmap]
rs7535765	0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7539415	0.85[CEU][hapmap]
rs7544221	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7554689	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs760603	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs925892	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs932301	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs994986	1.00[CHB][hapmap];0.82[JPT][hapmap]

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	esv10418	chr1:169059628-169621268	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Bivalent Enhancer 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	56 gene(s)	inside rSNPs	diseases
2	nsv831871	chr1:169320673-169486680	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv1001454	chr1:169387381-169465274	Enhancers Active TSS Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	26 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3820059	NME7	cis	Esophagus Muscularis	GTEx
rs3820059	SELP	cis	cerebellum	SCAN
rs3820059	NME7	Cis_1M	lymphoblastoid	RTeQTL
rs3820059	KIFAP3	cis	cerebellum	SCAN
rs3820059	NME7	cis	Artery Tibial	GTEx
rs3820059	C1orf114	cis	cerebellum	SCAN
rs3820059	NME7	cis	Thyroid	GTEx
rs3820059	C1orf114	cis	parietal	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:169360800-169395200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr1:169382000-169395200	Weak transcription	Brain Inferior Temporal Lobe	brain
3	chr1:169383600-169395400	Weak transcription	Ovary	ovary
4	chr1:169385000-169395200	Weak transcription	Brain Angular Gyrus	brain
5	chr1:169385400-169394800	Weak transcription	Brain Germinal Matrix	brain
6	chr1:169385600-169395200	Weak transcription	Brain Cingulate Gyrus	brain
7	chr1:169385600-169395600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr1:169385600-169395800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
9	chr1:169387000-169395800	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr1:169387800-169395400	Weak transcription	Brain Substantia Nigra	brain
11	chr1:169389000-169395400	Weak transcription	Fetal Brain Female	brain
12	chr1:169389200-169394000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr1:169389600-169394600	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr1:169390800-169391600	Strong transcription	Brain Anterior Caudate	brain
15	chr1:169391000-169395600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr1:169391000-169395600	Weak transcription	Fetal Heart	heart

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