Variant report

Variant	rs4664490
Chromosome Location	chr2:152471923-152471924
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 30 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs10167358	0.89[ASW][hapmap];0.86[CHB][hapmap];0.88[GIH][hapmap];0.82[ASN][1000 genomes]
rs10172023	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10173699	0.80[CHB][hapmap];0.88[GIH][hapmap]
rs10174077	0.92[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs10186656	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1047957	0.80[CHB][hapmap]
rs10497082	0.80[CHB][hapmap]
rs11892439	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13425170	0.82[JPT][hapmap]
rs2432946	0.80[CHB][hapmap]
rs2432956	0.80[CHB][hapmap]
rs2432957	0.80[CHB][hapmap]
rs2444264	0.80[CHB][hapmap]
rs3771901	0.89[ASW][hapmap];0.84[GIH][hapmap];0.82[ASN][1000 genomes]
rs4461258	0.89[ASW][hapmap];0.87[CHB][hapmap];0.88[GIH][hapmap];0.88[JPT][hapmap];0.82[ASN][1000 genomes]
rs4592848	0.80[CHB][hapmap];0.88[GIH][hapmap]
rs4664491	0.93[CHB][hapmap];1.00[JPT][hapmap];0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6750342	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[CHB][hapmap];0.92[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MEX][hapmap];0.97[MKK][hapmap];0.98[TSI][hapmap];0.90[YRI][hapmap];0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[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	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	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
6	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
7	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
8	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
9	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
10	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
11	esv1799814	chr2:152435851-152472667	Enhancers Weak transcription Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	esv1795796	chr2:152436051-152477968	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4664490	RIF1	cis	parietal	SCAN
rs4664490	RND3	cis	parietal	SCAN
rs4664490	SNORA49	trans	parietal	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:152460600-152489200	Weak transcription	Psoas Muscle	Psoas
2	chr2:152465400-152478200	Strong transcription	Fetal Muscle Leg	muscle
3	chr2:152465400-152491400	Weak transcription	Primary B cells from cord blood	blood
4	chr2:152467800-152491400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr2:152470400-152477600	Strong transcription	HSMMtube	muscle
6	chr2:152470600-152472000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr2:152470600-152472000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
8	chr2:152470600-152472000	Genic enhancers	Skeletal Muscle Female	skeletal muscle
9	chr2:152470600-152472400	Enhancers	HUVEC	blood vessel
10	chr2:152470600-152474000	Strong transcription	Fetal Muscle Trunk	muscle
11	chr2:152470800-152472000	Enhancers	Primary T helper cells PMA-I stimulated	--
12	chr2:152470800-152472000	Enhancers	K562	blood
13	chr2:152471000-152472000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
14	chr2:152471000-152472200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
15	chr2:152471000-152472200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
16	chr2:152471200-152472000	Enhancers	Primary T helper cells fromperipheralblood	blood
17	chr2:152471200-152472000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr2:152471200-152472000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
19	chr2:152471200-152472200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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