Variant report

Variant	rs13406354
Chromosome Location	chr2:134115804-134115805
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 91 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs10165601	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10171473	0.85[ASN][1000 genomes]
rs10175744	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.85[LWK][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10180047	1.00[CEU][hapmap];1.00[CHB][hapmap];0.86[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10182402	0.81[ASN][1000 genomes]
rs10182656	0.92[ASN][1000 genomes]
rs10184630	1.00[CEU][hapmap];1.00[CHB][hapmap];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10191826	0.87[CEU][hapmap];0.86[CHB][hapmap];0.86[ASN][1000 genomes]
rs10193087	0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10193730	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10196395	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204436	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10204527	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10206474	0.85[ASN][1000 genomes]
rs10469580	0.90[ASN][1000 genomes]
rs10928450	0.81[ASN][1000 genomes]
rs10928451	0.89[ASN][1000 genomes]
rs11884182	0.82[ASN][1000 genomes]
rs11890293	0.85[CEU][hapmap];0.86[CHB][hapmap];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11898252	0.84[ASN][1000 genomes]
rs12327930	0.88[CHB][hapmap];0.85[ASN][1000 genomes]
rs12328723	1.00[CEU][hapmap];0.88[CHB][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12328976	0.87[CEU][hapmap];1.00[CHB][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13392963	0.88[ASN][1000 genomes]
rs13396831	1.00[CHB][hapmap];0.88[CHD][hapmap];0.91[GIH][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13396930	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs13400561	0.85[ASN][1000 genomes]
rs13400743	1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs13406057	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs13407205	0.87[CEU][hapmap];0.88[CHB][hapmap];0.94[ASN][1000 genomes]
rs13407503	0.87[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.98[ASN][1000 genomes]
rs13408835	1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs13409478	0.93[CEU][hapmap]
rs13411233	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.86[GIH][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13412956	1.00[CHB][hapmap];0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13414823	0.93[CEU][hapmap];0.81[ASN][1000 genomes]
rs13421761	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13426157	0.88[CHB][hapmap];0.94[CHD][hapmap];0.88[GIH][hapmap];0.97[TSI][hapmap];0.91[ASN][1000 genomes]
rs13426681	0.88[CHB][hapmap];0.91[ASN][1000 genomes]
rs13432602	1.00[ASW][hapmap];0.93[CEU][hapmap];0.86[CHB][hapmap];0.88[CHD][hapmap];0.82[GIH][hapmap];0.92[JPT][hapmap];0.89[MEX][hapmap];0.92[MKK][hapmap];0.90[TSI][hapmap];0.80[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1346776	1.00[CEU][hapmap];0.86[CHB][hapmap];0.82[GIH][hapmap];0.94[TSI][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1369509	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap]
rs1369510	0.82[ASW][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1430165	0.93[CEU][hapmap];0.84[TSI][hapmap];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1430166	0.93[CEU][hapmap];0.86[CHB][hapmap];0.90[TSI][hapmap];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1430167	0.81[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1430168	1.00[CEU][hapmap];1.00[CHB][hapmap];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1435554	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1435556	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1435563	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1435564	0.88[CHB][hapmap];0.84[ASN][1000 genomes]
rs1435565	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1435566	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1561018	0.88[CHB][hapmap];0.93[TSI][hapmap];0.84[ASN][1000 genomes]
rs16824299	0.88[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs16824301	0.89[ASN][1000 genomes]
rs16824303	0.89[ASN][1000 genomes]
rs16824511	1.00[CHB][hapmap];0.86[ASN][1000 genomes]
rs16824573	0.84[ASN][1000 genomes]
rs17745593	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[ASN][1000 genomes]
rs17745851	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17802295	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.86[GIH][hapmap];0.84[MEX][hapmap];1.00[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1898008	1.00[CHB][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2115864	0.85[ASN][1000 genomes]
rs2289075	0.88[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[ASN][1000 genomes]
rs2304404	0.93[CEU][hapmap];0.88[CHB][hapmap];0.84[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28445548	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35892150	0.81[ASN][1000 genomes]
rs4588241	0.88[ASN][1000 genomes]
rs55788182	0.91[ASN][1000 genomes]
rs56410092	0.89[ASN][1000 genomes]
rs58489491	0.86[ASN][1000 genomes]
rs62177662	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62177669	0.93[ASN][1000 genomes]
rs62177672	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs62180011	0.88[ASN][1000 genomes]
rs62180012	0.88[ASN][1000 genomes]
rs62180016	0.92[ASN][1000 genomes]
rs62180017	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7573164	0.88[CHB][hapmap];0.89[ASN][1000 genomes]
rs9287426	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.86[GIH][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9808392	0.93[CEU][hapmap];0.81[ASN][1000 genomes]
rs990476	0.88[CHB][hapmap];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv997821	chr2:133868822-134360220	ZNF genes & repeats Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
2	nsv535927	chr2:133868822-134360220	Weak transcription Enhancers Active TSS Bivalent Enhancer Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	24 gene(s)	inside rSNPs	diseases
3	nsv1002488	chr2:133890159-134275312	Weak transcription Enhancers Strong transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
4	nsv535928	chr2:133890159-134275312	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Bivalent/Poised TSS Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
5	esv3375790	chr2:133906915-134222833	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834384	chr2:134005229-134188648	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
7	nsv1014718	chr2:134067133-134151633	Enhancers Weak transcription Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
8	nsv522324	chr2:134085665-134174032	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:4 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:134104400-134118600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr2:134111800-134117800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr2:134114200-134116400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:134115400-134116000	Enhancers	Hela-S3	cervix

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links