Variant report

Variant	rs13425109
Chromosome Location	chr2:152394106-152394107
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152389412..152391698-chr2:152393142..152395709,2	MCF-7	breast:
2	chr2:152392031..152396031-chr2:152396144..152400510,4	K562	blood:
3	chr2:152392901..152394420-chr2:152407078..152409911,2	K562	blood:

Variant related genes	Relation type
ENSG00000183091	Chromatin interaction

Extended variants
information (count: 66 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10174130	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs10182296	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10187997	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10210564	0.82[AMR][1000 genomes]
rs10432479	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10930688	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs13391309	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830136	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288195	0.83[EUR][1000 genomes]
rs2288196	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2288198	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2288201	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2288202	0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs2288203	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3213818	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34829854	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3732310	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3771900	0.83[EUR][1000 genomes]
rs3815852	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233649	0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233650	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4233651	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4233652	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4372897	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4575719	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs4643540	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664055	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4664056	0.82[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664455	0.83[EUR][1000 genomes]
rs4664475	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4664485	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664486	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4994327	0.83[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs60806638	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6414089	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6433469	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6433481	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6433482	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6704618	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719297	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs6721666	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6725513	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6730454	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735678	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6744470	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419956	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7558940	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7563568	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7566225	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7575451	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7585717	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs7597735	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7602828	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs9287979	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9287981	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9287982	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9287983	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013484	chr2:152028515-152473913	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
2	nsv535983	chr2:152028515-152473913	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
3	nsv999748	chr2:152135514-152476396	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	12 gene(s)	inside rSNPs	diseases
4	nsv934136	chr2:152308156-152664443	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	esv3693428	chr2:152320932-152434896	Strong transcription Weak transcription Enhancers Active TSS ZNF genes & repeats Genic enhancers Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv1005746	chr2:152361972-153059840	Strong transcription Weak transcription Bivalent/Poised TSS Enhancers Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
7	nsv535984	chr2:152361972-153059840	Active TSS Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
8	esv1793381	chr2:152370040-152463631	Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
9	nsv10198	chr2:152370068-152463644	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs13425109	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs13425109	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs13425109	RIF1	cis	Artery Tibial	GTEx

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152343200-152422200	Weak transcription	Primary B cells from cord blood	blood
2	chr2:152348800-152400800	Strong transcription	Skeletal Muscle Female	skeletal muscle
3	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
4	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
5	chr2:152370400-152403600	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:152371400-152421000	Weak transcription	Pancreas	Pancrea
7	chr2:152381000-152398000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr2:152381000-152410200	Weak transcription	Placenta	Placenta
9	chr2:152383200-152424000	Weak transcription	Primary B cells from peripheral blood	blood
10	chr2:152383400-152396400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:152385800-152426800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
12	chr2:152389000-152399200	Weak transcription	Ovary	ovary
13	chr2:152389600-152394800	Weak transcription	Brain Hippocampus Middle	brain
14	chr2:152389800-152412000	Strong transcription	HSMMtube	muscle
15	chr2:152391000-152405600	Weak transcription	Left Ventricle	heart
16	chr2:152392000-152405200	Weak transcription	Brain Angular Gyrus	brain
17	chr2:152392600-152401000	Weak transcription	Aorta	Aorta
18	chr2:152392600-152414200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:152392800-152396800	Weak transcription	Psoas Muscle	Psoas
20	chr2:152393800-152395000	Weak transcription	Fetal Muscle Trunk	muscle
21	chr2:152393800-152395800	Weak transcription	Fetal Muscle Leg	muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links