Variant report

Variant	rs7558940
Chromosome Location	chr2:152368055-152368056
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	chr2:152366454..152368368-chr2:152374730..152376370,2	MCF-7	breast:

Extended variants
information (count: 95 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10174130	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs10182296	1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10187997	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10210564	0.84[AMR][1000 genomes]
rs10432479	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.96[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065177	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.92[ASN][1000 genomes]
rs10930688	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13002073	0.80[ASN][1000 genomes]
rs13391309	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13425109	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16830136	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2123465	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2288195	0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2288196	0.84[CEU][hapmap];0.93[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2288198	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2288201	0.89[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2288203	0.90[EUR][1000 genomes]
rs2288210	0.80[YRI][hapmap]
rs2432936	0.93[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2432938	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs2432940	0.80[ASN][1000 genomes]
rs2432941	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2432944	0.80[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2432951	1.00[CHB][hapmap];0.86[JPT][hapmap];0.93[YRI][hapmap];0.80[ASN][1000 genomes]
rs2444257	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2444259	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs2444260	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs2444262	0.82[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs2444263	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2444266	0.88[ASN][1000 genomes]
rs2444270	1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.80[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs2444272	0.90[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.82[AFR][1000 genomes];0.90[ASN][1000 genomes]
rs2444274	0.92[CHB][hapmap];0.93[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3213818	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34829854	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3732310	0.84[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3771900	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3815851	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.92[ASN][1000 genomes]
rs3815852	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4233649	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4233650	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4233651	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4233652	0.92[EUR][1000 genomes]
rs4315520	0.86[JPT][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs4372897	0.80[EUR][1000 genomes]
rs4474880	0.84[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4643540	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4664055	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4664056	0.88[CEU][hapmap];0.90[EUR][1000 genomes]
rs4664065	0.84[CHB][hapmap]
rs4664455	1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4664475	0.88[CEU][hapmap];0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs4664485	0.87[EUR][1000 genomes]
rs4664486	0.88[CEU][hapmap];0.92[EUR][1000 genomes]
rs4664493	0.82[CHB][hapmap]
rs4994327	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs60806638	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6414089	1.00[CEU][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6433469	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6433481	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6433482	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6704618	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6707824	0.84[CHB][hapmap]
rs6715917	0.81[ASN][1000 genomes]
rs6719297	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6721666	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6725513	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6730454	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6735678	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6744470	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7419413	0.83[YRI][hapmap]
rs7419956	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.89[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7422136	0.82[CHB][hapmap]
rs7424331	0.83[YRI][hapmap]
rs7563568	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7566225	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7575451	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7585717	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7597735	0.89[CEU][hapmap];0.93[JPT][hapmap];0.87[YRI][hapmap];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7602828	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9287979	0.89[CEU][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9287981	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287982	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.80[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9287983	0.88[CEU][hapmap];0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 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

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7558940	RIF1	cis	Artery Tibial	GTEx
rs7558940	RIF1	Cis_1M	lymphoblastoid	RTeQTL
rs7558940	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152267600-152379400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:152324200-152382400	Weak transcription	Aorta	Aorta
3	chr2:152338200-152370000	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:152340400-152371000	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr2:152341600-152390600	Weak transcription	Left Ventricle	heart
6	chr2:152343200-152422200	Weak transcription	Primary B cells from cord blood	blood
7	chr2:152343400-152371000	Weak transcription	Adipose Nuclei	Adipose
8	chr2:152343400-152373000	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr2:152346200-152370000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr2:152347000-152387200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr2:152348600-152369600	Weak transcription	K562	blood
12	chr2:152348800-152400800	Strong transcription	Skeletal Muscle Female	skeletal muscle
13	chr2:152349400-152370000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:152355400-152368200	Weak transcription	HUES48 Cell Line	embryonic stem cell
15	chr2:152356200-152369200	Weak transcription	H1 Cell Line	embryonic stem cell
16	chr2:152358600-152394000	Weak transcription	Spleen	Spleen
17	chr2:152359400-152382200	Weak transcription	Primary B cells from peripheral blood	blood
18	chr2:152359800-152376400	Strong transcription	Fetal Muscle Trunk	muscle
19	chr2:152360400-152376000	Strong transcription	Fetal Muscle Leg	muscle
20	chr2:152360800-152424400	Weak transcription	Brain Anterior Caudate	brain
21	chr2:152361000-152387800	Strong transcription	HSMMtube	muscle
22	chr2:152363200-152391800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:152364600-152377600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
24	chr2:152365200-152385200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr2:152365200-152415600	Weak transcription	Fetal Intestine Small	intestine
26	chr2:152365400-152377000	Weak transcription	Placenta	Placenta
27	chr2:152365400-152377600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
28	chr2:152367400-152370400	Strong transcription	Psoas Muscle	Psoas
29	chr2:152367800-152368600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell

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