Variant report

Variant	rs6721666
Chromosome Location	chr2:152382454-152382455
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:63)

rs_ID	r²[population]
rs10174130	0.81[EUR][1000 genomes]
rs10182296	0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10186482	0.85[JPT][hapmap]
rs10187997	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs10210564	0.83[AMR][1000 genomes]
rs10432479	1.00[CEU][hapmap];0.83[YRI][hapmap];0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1047957	0.87[YRI][hapmap]
rs1061305	0.86[YRI][hapmap]
rs10930688	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13391309	0.88[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13425109	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16830136	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288196	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2288198	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288201	0.81[EUR][1000 genomes]
rs2288202	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2288203	0.89[ASN][1000 genomes]
rs2432946	0.86[YRI][hapmap]
rs2432956	0.87[YRI][hapmap]
rs2432957	0.86[YRI][hapmap]
rs2444264	0.86[YRI][hapmap]
rs3213818	0.81[EUR][1000 genomes]
rs34829854	0.80[EUR][1000 genomes]
rs3732310	0.96[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3815852	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233649	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233650	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4233651	0.83[CEU][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs4233652	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4372897	0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4575719	0.89[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4643540	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664055	0.84[CEU][hapmap];0.81[EUR][1000 genomes]
rs4664056	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4664475	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4664485	0.93[ASN][1000 genomes]
rs4664486	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4994327	0.82[CEU][hapmap];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs60806638	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6414089	0.89[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6433469	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6433481	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433482	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6704618	0.89[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6718372	0.87[YRI][hapmap]
rs6719297	0.96[CEU][hapmap];0.83[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6720169	0.90[JPT][hapmap]
rs6725513	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6730454	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.99[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6735678	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6744470	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7419956	0.93[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7558940	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7563568	0.81[EUR][1000 genomes]
rs7566225	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7575451	0.89[CEU][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7585717	0.84[CEU][hapmap];0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs7597735	1.00[CEU][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7602828	0.81[EUR][1000 genomes]
rs9287979	1.00[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9287981	0.89[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9287982	0.88[CEU][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs9287983	0.84[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.81[EUR][1000 genomes];0.92[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	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	nsv834418	chr2:152205803-152385516	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	9 gene(s)	inside rSNPs	diseases
7	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
8	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
9	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
10	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
11	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
12	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
13	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
rs6721666	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:30 , 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	chr2:152347000-152387200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr2:152348800-152400800	Strong transcription	Skeletal Muscle Female	skeletal muscle
5	chr2:152358600-152394000	Weak transcription	Spleen	Spleen
6	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
7	chr2:152361000-152387800	Strong transcription	HSMMtube	muscle
8	chr2:152363200-152391800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
9	chr2:152365200-152385200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
10	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
11	chr2:152370400-152403600	Strong transcription	Skeletal Muscle Male	skeletal muscle
12	chr2:152371400-152421000	Weak transcription	Pancreas	Pancrea
13	chr2:152374200-152385600	Weak transcription	Psoas Muscle	Psoas
14	chr2:152377200-152391800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr2:152377400-152393800	Strong transcription	Fetal Muscle Leg	muscle
16	chr2:152378000-152386600	Weak transcription	H9 Cell Line	embryonic stem cell
17	chr2:152378400-152390600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
18	chr2:152380200-152388400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:152380400-152388200	Weak transcription	Right Ventricle	heart
20	chr2:152381000-152398000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr2:152381000-152410200	Weak transcription	Placenta	Placenta
22	chr2:152382200-152383200	Enhancers	Primary B cells from peripheral blood	blood
23	chr2:152382200-152383200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
24	chr2:152382400-152382600	ZNF genes & repeats	Aorta	Aorta
25	chr2:152382400-152382600	ZNF genes & repeats	Esophagus	oesophagus
26	chr2:152382400-152382800	Flanking Active TSS	Primary neutrophils fromperipheralblood	blood
27	chr2:152382400-152382800	Enhancers	Primary hematopoietic stem cells	blood
28	chr2:152382400-152382800	Enhancers	Primary hematopoietic stem cells short term culture	blood
29	chr2:152382400-152382800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr2:152382400-152382800	Enhancers	Monocytes-CD14+_RO01746	blood

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