Variant report

Variant	rs7422136
Chromosome Location	chr2:152434317-152434318
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 78 )
Associated
traits (count: 5 )

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

rs_ID	r²[population]
rs10174130	0.84[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs10182296	0.81[CHB][hapmap]
rs10186482	0.80[CEU][hapmap]
rs10187997	0.82[CHB][hapmap];0.85[JPT][hapmap];0.89[YRI][hapmap]
rs10210564	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10432479	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs1065177	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs10930688	0.82[CHB][hapmap]
rs12996964	0.90[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs13383484	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13391309	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2123465	0.92[CHD][hapmap];0.82[YRI][hapmap]
rs2288195	0.92[CHD][hapmap]
rs2288198	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs2288201	0.80[CEU][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs2288203	0.81[AMR][1000 genomes]
rs2288210	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2432936	0.82[YRI][hapmap]
rs2432938	0.82[CHB][hapmap];0.92[CHD][hapmap]
rs2432941	0.88[CHD][hapmap];0.82[YRI][hapmap]
rs2432951	0.82[CHB][hapmap];0.92[JPT][hapmap];0.81[YRI][hapmap]
rs2444257	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs2444259	0.82[CHB][hapmap]
rs2444260	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs2444263	0.92[CHD][hapmap];0.82[YRI][hapmap]
rs2444270	0.82[CHB][hapmap];0.82[YRI][hapmap]
rs2444272	0.92[YRI][hapmap]
rs2444274	0.92[CHD][hapmap];0.82[YRI][hapmap]
rs3213818	0.83[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34829854	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs3815851	0.88[CHD][hapmap];0.82[YRI][hapmap]
rs3815852	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs4233651	1.00[CHB][hapmap];0.84[JPT][hapmap]
rs4315520	0.82[CHD][hapmap];0.92[JPT][hapmap];0.82[YRI][hapmap]
rs4664055	0.81[CEU][hapmap];0.82[CHB][hapmap];0.96[CHD][hapmap];1.00[LWK][hapmap];0.95[MEX][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs4664056	0.81[CEU][hapmap];0.85[MEX][hapmap];0.81[AMR][1000 genomes]
rs4664064	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4664065	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4664455	0.82[CHB][hapmap];0.96[CHD][hapmap];0.82[YRI][hapmap]
rs4664486	0.81[CEU][hapmap];0.85[MEX][hapmap];0.80[AMR][1000 genomes]
rs4664493	0.81[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs4994327	0.82[YRI][hapmap]
rs6433481	0.82[CHB][hapmap]
rs6433482	0.81[CHB][hapmap];0.89[YRI][hapmap]
rs6707824	0.84[JPT][hapmap]
rs6709886	0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6719297	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs6720169	0.84[CEU][hapmap]
rs6725513	0.84[YRI][hapmap]
rs6732307	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6735678	0.82[CHB][hapmap];0.92[CHD][hapmap];0.95[LWK][hapmap];0.86[MKK][hapmap];0.89[YRI][hapmap]
rs7419413	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7419956	0.82[CHB][hapmap];0.88[CHD][hapmap]
rs7421893	0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7424331	0.89[YRI][hapmap];0.83[AFR][1000 genomes];0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7558940	0.82[CHB][hapmap]
rs7563568	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs7568873	1.00[CEU][hapmap];0.90[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7585717	0.82[CHB][hapmap];0.96[CHD][hapmap]
rs7602828	0.81[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs9287981	0.81[CHB][hapmap];0.89[YRI][hapmap]
rs9287982	0.82[CHB][hapmap];0.92[CHD][hapmap];0.97[LWK][hapmap];0.85[MKK][hapmap];0.89[YRI][hapmap]
rs9287983	0.81[CEU][hapmap];0.85[MEX][hapmap]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv963734	chr2:152433475-152466257	Strong transcription Enhancers Weak transcription Genic enhancers	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
14	esv1797169	chr2:152433970-152466350	Genic enhancers Enhancers Strong transcription Weak transcription	TF binding region CpG island	1 gene(s)	inside rSNPs	diseases
15	esv1800583	chr2:152433970-152480935	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs7422136	RIF1	cis	parietal	SCAN
rs7422136	SNORA49	trans	parietal	SCAN
rs7422136	RIF1	cis	Skin Sun Exposed Lower leg	GTEx
rs7422136	LYPD6	cis	parietal	SCAN
rs7422136	RND3	cis	parietal	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152409400-152437000	Weak transcription	Psoas Muscle	Psoas
2	chr2:152416200-152434400	Strong transcription	Fetal Muscle Leg	muscle
3	chr2:152434000-152434800	Strong transcription	Skeletal Muscle Male	skeletal muscle
4	chr2:152434000-152466200	Weak transcription	Fetal Muscle Trunk	muscle
5	chr2:152434200-152434800	Strong transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:152434200-152448200	Weak transcription	HSMMtube	muscle

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