Variant report

Variant	rs12064403
Chromosome Location	chr1:174596205-174596206
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:174585484..174588132-chr1:174595447..174597220,2	K562	blood:

Extended variants
information (count: 117 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:110)

rs_ID	r²[population]
rs10489264	0.92[ASN][1000 genomes]
rs10912817	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912820	0.80[AMR][1000 genomes]
rs10912821	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912822	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912823	0.89[ASN][1000 genomes]
rs10912828	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10912829	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11487400	0.91[ASN][1000 genomes]
rs11487401	0.91[ASN][1000 genomes]
rs11802092	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11805578	0.92[ASN][1000 genomes]
rs11806996	0.86[EUR][1000 genomes]
rs12062016	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12063545	0.92[ASN][1000 genomes]
rs12064749	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12065825	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12067463	0.89[ASN][1000 genomes]
rs12079118	0.92[ASN][1000 genomes]
rs12079757	0.85[ASN][1000 genomes]
rs12079879	0.92[ASN][1000 genomes]
rs12080535	0.89[ASN][1000 genomes]
rs12082012	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12082139	0.89[ASN][1000 genomes]
rs12083628	0.89[ASN][1000 genomes]
rs12085652	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1474575	0.92[ASN][1000 genomes]
rs149099	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs16847335	0.86[ASN][1000 genomes]
rs16847337	0.86[ASN][1000 genomes]
rs17842156	0.86[ASN][1000 genomes]
rs17842157	0.86[ASN][1000 genomes]
rs193082	0.82[AMR][1000 genomes]
rs2060158	0.86[ASN][1000 genomes]
rs2092084	0.92[ASN][1000 genomes]
rs2142632	0.92[ASN][1000 genomes]
rs2146564	0.86[ASN][1000 genomes]
rs2568098	0.82[AMR][1000 genomes]
rs2760058	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2771401	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs2861003	0.92[ASN][1000 genomes]
rs2861005	0.86[ASN][1000 genomes]
rs2861006	0.86[ASN][1000 genomes]
rs3117838	0.81[AMR][1000 genomes]
rs3117843	0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs332763	0.84[ASN][1000 genomes]
rs332764	0.84[ASN][1000 genomes]
rs332767	0.85[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs332768	0.88[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs332772	0.84[ASN][1000 genomes]
rs332779	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs332781	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs332782	0.84[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs332786	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs332793	0.81[AMR][1000 genomes]
rs332800	0.81[AMR][1000 genomes]
rs332801	0.81[AMR][1000 genomes]
rs332802	0.93[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs332804	0.88[AMR][1000 genomes]
rs332806	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs333422	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs333423	0.84[ASN][1000 genomes]
rs333432	0.81[AMR][1000 genomes]
rs333436	0.81[AMR][1000 genomes]
rs333437	0.84[ASN][1000 genomes]
rs333438	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs333452	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs333454	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs333471	0.84[ASN][1000 genomes]
rs34409674	0.92[ASN][1000 genomes]
rs3862941	0.86[ASN][1000 genomes]
rs3920486	0.86[ASN][1000 genomes]
rs395109	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs398350	0.87[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs399530	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs411665	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4451598	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4562683	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs458242	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4615901	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs464540	0.89[AMR][1000 genomes];0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs464635	0.81[AMR][1000 genomes]
rs4651103	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4651114	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4652652	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4652669	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs467437	0.89[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs55643907	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs55667039	0.86[ASN][1000 genomes]
rs55688014	0.86[ASN][1000 genomes]
rs55945681	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56260545	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs61624206	0.89[ASN][1000 genomes]
rs6667107	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6675515	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6677874	0.89[ASN][1000 genomes]
rs6689153	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6691118	0.89[ASN][1000 genomes]
rs72715240	0.89[ASN][1000 genomes]
rs72715245	0.92[ASN][1000 genomes]
rs72715253	0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715255	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715259	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715260	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715262	0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72715273	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7414200	0.92[ASN][1000 genomes]
rs7516353	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7530265	0.89[ASN][1000 genomes]
rs7542775	0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014637	chr1:174265631-174826765	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv535208	chr1:174265631-174826765	Weak transcription ZNF genes & repeats Strong transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	nsv1014753	chr1:174271770-174694838	Weak transcription Strong transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
4	esv2755184	chr1:174388343-174970343	Flanking Active TSS Weak transcription Enhancers Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
5	nsv999295	chr1:174457532-174596961	Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
6	nsv534381	chr1:174468168-174656796	Weak transcription Enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv1803591	chr1:174594575-174642336	Enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12064403	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174572800-174606200	Weak transcription	Primary T cells fromperipheralblood	blood
2	chr1:174582800-174606400	Weak transcription	Primary T helper cells PMA-I stimulated	--
3	chr1:174587600-174606600	Weak transcription	Primary B cells from cord blood	blood
4	chr1:174587600-174609200	Weak transcription	Pancreas	Pancrea
5	chr1:174594600-174597400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
6	chr1:174595200-174597000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:174595400-174609400	Weak transcription	GM12878-XiMat	blood
8	chr1:174595600-174596600	Enhancers	Brain Hippocampus Middle	brain
9	chr1:174595600-174597400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
10	chr1:174595600-174609000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr1:174596000-174596800	Enhancers	Brain Inferior Temporal Lobe	brain
12	chr1:174596000-174597000	Weak transcription	Fetal Intestine Large	intestine
13	chr1:174596000-174598400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
14	chr1:174596000-174606800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links