Variant report

Variant	rs1653636
Chromosome Location	chr1:174736877-174736878
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:174735208..174740631-chr1:174966337..174969324,7	MCF-7	breast:
2	chr1:174735393..174743353-chr1:174964672..174971853,16	K562	blood:
3	chr1:174735485..174737469-chr1:174955783..174958399,2	K562	blood:
4	chr1:174736386..174740944-chr1:174964309..174969947,11	K562	blood:

Variant related genes	Relation type
ENSG00000252552	Chromatin interaction
ENSG00000116161	Chromatin interaction

Extended variants
information (count: 96 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs10494492	0.80[ASN][1000 genomes]
rs10798324	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10912820	0.83[EUR][1000 genomes]
rs10912823	0.86[EUR][1000 genomes]
rs10912854	0.81[EUR][1000 genomes]
rs12067463	0.86[EUR][1000 genomes]
rs12077529	0.80[EUR][1000 genomes]
rs12080535	0.82[EUR][1000 genomes]
rs12082139	0.85[EUR][1000 genomes]
rs12083628	0.82[EUR][1000 genomes]
rs1231829	0.84[EUR][1000 genomes]
rs1329281	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1613634	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1618207	0.83[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1618408	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1622802	0.89[AFR][1000 genomes];0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs162815	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1653630	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1653634	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1754354	0.85[ASN][1000 genomes]
rs1754360	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793292	0.83[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1793294	0.85[AFR][1000 genomes];0.83[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1793295	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs1793298	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs1793307	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793310	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1793313	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1793315	0.84[EUR][1000 genomes]
rs1793320	0.84[ASN][1000 genomes]
rs1813136	0.90[ASN][1000 genomes]
rs1894198	0.83[EUR][1000 genomes]
rs1894199	0.81[EUR][1000 genomes]
rs1923818	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs193082	0.81[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2163628	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs2568096	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2568098	0.90[ASN][1000 genomes]
rs2760057	0.83[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2981892	0.85[EUR][1000 genomes]
rs3117838	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs3118990	0.85[ASN][1000 genomes]
rs332763	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332764	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332772	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs332784	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs332787	0.84[ASN][1000 genomes]
rs332793	0.85[ASN][1000 genomes]
rs332797	0.85[ASN][1000 genomes]
rs332798	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs332800	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs332801	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs333423	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs333432	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs333436	0.81[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs333437	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs333453	0.86[EUR][1000 genomes]
rs333471	0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs392307	0.83[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs4359076	0.83[AFR][1000 genomes]
rs459078	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs460878	0.81[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs464635	0.87[ASN][1000 genomes]
rs4651205	0.81[EUR][1000 genomes]
rs4652797	0.90[ASN][1000 genomes]
rs55844798	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56292878	0.84[EUR][1000 genomes]
rs60811893	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61624206	0.82[EUR][1000 genomes]
rs6425303	0.80[EUR][1000 genomes]
rs6675528	0.81[EUR][1000 genomes]
rs6677874	0.86[EUR][1000 genomes]
rs6691118	0.82[EUR][1000 genomes]
rs6692173	0.80[EUR][1000 genomes]
rs6696465	0.89[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6700953	0.85[EUR][1000 genomes]
rs72715292	0.90[ASN][1000 genomes]
rs72715294	0.90[ASN][1000 genomes]
rs72715300	0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72717608	0.90[ASN][1000 genomes]
rs72717616	0.90[ASN][1000 genomes]
rs72717617	0.85[ASN][1000 genomes]
rs72717637	0.82[EUR][1000 genomes]
rs7514183	0.81[EUR][1000 genomes]
rs7521109	0.90[ASN][1000 genomes]
rs7530265	0.82[EUR][1000 genomes]
rs7542775	0.82[EUR][1000 genomes]
rs7554728	0.80[EUR][1000 genomes]
rs913687	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs913688	0.90[ASN][1000 genomes]
rs989424	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
4	nsv548197	chr1:174731596-174741017	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv548198	chr1:174731596-174800872	Enhancers Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1653636	RABGAP1L	cis	Esophagus Muscularis	GTEx

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:174711800-174745600	Weak transcription	Primary B cells from cord blood	blood
2	chr1:174720200-174739000	Weak transcription	GM12878-XiMat	blood
3	chr1:174723200-174739000	Weak transcription	Primary T cells from cord blood	blood
4	chr1:174734200-174737400	Weak transcription	Fetal Muscle Leg	muscle
5	chr1:174735800-174737000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr1:174736000-174737800	Enhancers	Liver	Liver
7	chr1:174736400-174737400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr1:174736400-174737400	Weak transcription	Fetal Intestine Small	intestine
9	chr1:174736400-174739800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:174736600-174737000	Weak transcription	Fetal Intestine Large	intestine
11	chr1:174736600-174737000	Weak transcription	Stomach Mucosa	stomach

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