Variant report

Variant	rs60806638
Chromosome Location	chr2:152388228-152388229
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:152382125..152384924-chr2:152385395..152388332,2	K562	blood:

Variant related genes	Relation type
ENSG00000183091	Chromatin interaction

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs10174130	0.80[EUR][1000 genomes]
rs10182296	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10187997	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10210564	0.80[AMR][1000 genomes]
rs10432479	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs10930688	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13391309	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13425109	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16830136	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288196	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2288198	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288201	0.80[EUR][1000 genomes]
rs2288202	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2288203	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3213818	0.80[EUR][1000 genomes]
rs3732310	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3815852	0.87[EUR][1000 genomes]
rs4233649	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233650	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233651	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4233652	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4372897	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4575719	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4643540	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4664055	0.80[EUR][1000 genomes]
rs4664056	0.81[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4664475	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4664485	0.80[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4664486	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4994327	0.85[EUR][1000 genomes]
rs6414089	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6433469	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6433481	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433482	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6704618	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6719297	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs6721666	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6725513	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6730454	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6735678	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6744470	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7419956	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7558940	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7563568	0.80[EUR][1000 genomes]
rs7566225	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7575451	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7585717	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7597735	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7602828	0.80[EUR][1000 genomes]
rs9287979	0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9287981	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9287982	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9287983	0.84[AMR][1000 genomes];0.80[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 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	nsv1012139	chr2:152114637-152389516	Strong transcription Weak transcription Enhancers Active TSS Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
4	nsv1011339	chr2:152114637-152392940	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
5	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
6	nsv933869	chr2:152308156-152391576	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs60806638	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152341600-152390600	Weak transcription	Left Ventricle	heart
2	chr2:152343200-152422200	Weak transcription	Primary B cells from cord blood	blood
3	chr2:152348800-152400800	Strong transcription	Skeletal Muscle Female	skeletal muscle
4	chr2:152358600-152394000	Weak transcription	Spleen	Spleen
5	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
6	chr2:152363200-152391800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
8	chr2:152370400-152403600	Strong transcription	Skeletal Muscle Male	skeletal muscle
9	chr2:152371400-152421000	Weak transcription	Pancreas	Pancrea
10	chr2:152377200-152391800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr2:152377400-152393800	Strong transcription	Fetal Muscle Leg	muscle
12	chr2:152378400-152390600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr2:152380200-152388400	Strong transcription	Fetal Muscle Trunk	muscle
14	chr2:152381000-152398000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
15	chr2:152381000-152410200	Weak transcription	Placenta	Placenta
16	chr2:152382800-152394000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr2:152383200-152392200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:152383200-152424000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr2:152383400-152396400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr2:152383800-152390000	Weak transcription	Aorta	Aorta
21	chr2:152385800-152426800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr2:152387600-152390600	Weak transcription	Psoas Muscle	Psoas
23	chr2:152387800-152389800	Weak transcription	HSMMtube	muscle

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