Variant report

Variant	rs4664493
Chromosome Location	chr2:152492324-152492325
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10182296	0.81[CHB][hapmap]
rs10186482	0.84[CEU][hapmap];0.91[TSI][hapmap];0.88[EUR][1000 genomes]
rs10187997	0.82[CHB][hapmap]
rs10432479	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs1065177	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs10930688	0.82[CHB][hapmap]
rs12996964	0.90[CHB][hapmap];0.96[CHD][hapmap];0.83[JPT][hapmap]
rs13383484	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13391309	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2123465	0.88[CHD][hapmap]
rs2288195	0.88[CHD][hapmap]
rs2288198	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2288210	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap]
rs2432938	0.82[CHB][hapmap];0.87[CHD][hapmap]
rs2432941	0.84[CHD][hapmap]
rs2444257	0.82[CHB][hapmap]
rs2444259	0.82[CHB][hapmap]
rs2444260	0.82[CHB][hapmap]
rs2444263	0.88[CHD][hapmap]
rs2444270	0.82[CHB][hapmap]
rs2444274	0.88[CHD][hapmap]
rs34579746	0.86[ASN][1000 genomes]
rs3815851	0.84[CHD][hapmap]
rs3815852	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs4233651	1.00[CHB][hapmap]
rs4664055	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs4664064	0.80[CEU][hapmap];0.81[EUR][1000 genomes]
rs4664065	0.92[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[YRI][hapmap];0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4664455	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs6433481	0.82[CHB][hapmap]
rs6433482	0.81[CHB][hapmap]
rs6709886	0.86[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6719297	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs6720169	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs6732307	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6735678	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7419413	0.90[CHB][hapmap];0.92[JPT][hapmap]
rs7419956	0.82[CHB][hapmap];0.85[CHD][hapmap]
rs7422136	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs7558940	0.82[CHB][hapmap]
rs7568873	0.81[CEU][hapmap];0.90[CHB][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs7585717	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs9287981	0.81[CHB][hapmap]
rs9287982	0.82[CHB][hapmap];0.87[CHD][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	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
4	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
5	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
6	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4664493	RIF1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152482000-152502400	Strong transcription	Fetal Muscle Leg	muscle
2	chr2:152482000-152507600	Strong transcription	Fetal Muscle Trunk	muscle
3	chr2:152482800-152493800	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr2:152482800-152494800	Weak transcription	Gastric	stomach
5	chr2:152485400-152492400	Strong transcription	Skeletal Muscle Male	skeletal muscle
6	chr2:152488600-152499400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr2:152489600-152505200	Strong transcription	HSMMtube	muscle
8	chr2:152490000-152492600	Weak transcription	Primary T helper cells fromperipheralblood	blood
9	chr2:152490200-152492600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:152490400-152492600	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr2:152490400-152492600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr2:152490400-152492800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr2:152490600-152493400	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr2:152490800-152494600	Strong transcription	Skeletal Muscle Female	skeletal muscle
15	chr2:152491400-152493600	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr2:152491800-152494600	Weak transcription	Osteobl	bone
17	chr2:152492000-152492400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
18	chr2:152492000-152493400	Weak transcription	Primary B cells from cord blood	blood
19	chr2:152492000-152493600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr2:152492000-152504000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
21	chr2:152492000-152506800	Weak transcription	Psoas Muscle	Psoas
22	chr2:152492200-152492600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
23	chr2:152492200-152493400	Enhancers	Primary hematopoietic stem cells short term culture	blood
24	chr2:152492200-152493600	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr2:152492200-152494000	Weak transcription	Fetal Stomach	stomach

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