Variant report

Variant	rs4575719
Chromosome Location	chr2:152409809-152409810
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:152392901..152394420-chr2:152407078..152409911,2	K562	blood:
2	chr2:152396825..152398789-chr2:152409057..152411603,2	K562	blood:
3	chr2:152402480..152405227-chr2:152409026..152411315,2	K562	blood:

Variant related genes	Relation type
ENSG00000183091	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10174130	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs10182296	0.91[EUR][1000 genomes]
rs10186482	0.85[JPT][hapmap]
rs10432479	0.88[CEU][hapmap];0.91[EUR][1000 genomes]
rs13425109	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs16830136	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288196	0.88[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2288201	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2288202	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288203	0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288210	0.83[AMR][1000 genomes]
rs3213818	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs34829854	0.87[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3732310	0.92[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4233652	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4372897	0.99[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4643540	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664055	0.88[CEU][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs4664056	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664057	1.00[YRI][hapmap];0.80[AFR][1000 genomes]
rs4664064	0.81[AMR][1000 genomes]
rs4664065	0.82[CEU][hapmap]
rs4664475	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664485	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4664486	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56224718	0.80[AFR][1000 genomes]
rs60806638	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6414089	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.85[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs6433469	0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6704618	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs6719297	0.84[CEU][hapmap];0.90[EUR][1000 genomes]
rs6720169	0.84[CEU][hapmap];0.90[JPT][hapmap]
rs6721666	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6730454	0.89[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6744470	0.84[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs7419413	0.83[AMR][1000 genomes]
rs7563568	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7597735	0.89[CEU][hapmap];0.91[EUR][1000 genomes]
rs7602828	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9287979	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287983	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 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
10	nsv2974	chr2:152401495-152499455	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
11	nsv469804	chr2:152404429-152570882	Strong transcription Enhancers Weak transcription Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv482520	chr2:152404429-152570882	Weak transcription Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
13	nsv932914	chr2:152408090-152425360	Weak transcription Strong transcription Enhancers Genic enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4575719	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:17 , 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	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
3	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
4	chr2:152371400-152421000	Weak transcription	Pancreas	Pancrea
5	chr2:152381000-152410200	Weak transcription	Placenta	Placenta
6	chr2:152383200-152424000	Weak transcription	Primary B cells from peripheral blood	blood
7	chr2:152385800-152426800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr2:152389800-152412000	Strong transcription	HSMMtube	muscle
9	chr2:152392600-152414200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
10	chr2:152395000-152411800	Strong transcription	Fetal Muscle Trunk	muscle
11	chr2:152395800-152411800	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:152406000-152425800	Weak transcription	Aorta	Aorta
13	chr2:152408000-152410600	Weak transcription	Primary T helper cells fromperipheralblood	blood
14	chr2:152408400-152412600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr2:152409400-152411400	Genic enhancers	Skeletal Muscle Male	skeletal muscle
16	chr2:152409400-152437000	Weak transcription	Psoas Muscle	Psoas
17	chr2:152409800-152410000	Genic enhancers	Skeletal Muscle Female	skeletal muscle

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