Variant report

Variant	rs1550343
Chromosome Location	chr3:61159488-61159489
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 76 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1001788	0.89[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10049007	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049287	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049452	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10049454	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10866045	0.98[EUR][1000 genomes]
rs11130820	0.87[EUR][1000 genomes]
rs11707984	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11712122	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12053817	1.00[ASW][hapmap];0.81[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.89[MKK][hapmap];0.96[YRI][hapmap];0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12635622	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13099397	0.90[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.80[ASN][1000 genomes]
rs13320646	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13323296	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1371095	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1473644	0.83[ASN][1000 genomes]
rs1554601	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1866433	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1866434	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs1880213	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs1916802	0.81[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs1966136	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap]
rs1969420	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2118811	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2886377	1.00[ASW][hapmap];0.92[CEU][hapmap];0.89[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];1.00[LWK][hapmap];0.87[MEX][hapmap];0.87[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34045993	0.81[ASN][1000 genomes]
rs4296587	0.80[ASN][1000 genomes]
rs4309721	0.89[ASW][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];0.85[JPT][hapmap];0.93[LWK][hapmap];0.83[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs4535219	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs4688295	0.96[ASN][1000 genomes]
rs4688310	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4688379	0.83[ASN][1000 genomes]
rs56076618	0.97[AFR][1000 genomes];0.90[AMR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61275795	0.92[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs62268809	0.88[EUR][1000 genomes]
rs6445196	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6787511	0.92[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6807748	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6809031	0.82[ASN][1000 genomes]
rs753661	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs753662	0.97[EUR][1000 genomes]
rs7631101	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7631246	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7636682	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7641177	1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7647122	0.84[CHB][hapmap];0.88[JPT][hapmap];0.84[ASN][1000 genomes]
rs7653719	0.88[AFR][1000 genomes];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs9311799	0.86[EUR][1000 genomes]
rs9811478	0.81[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs9814044	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816087	0.99[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs9819588	0.94[ASW][hapmap];0.94[LWK][hapmap];0.96[YRI][hapmap];0.85[AFR][1000 genomes]
rs9827045	0.98[EUR][1000 genomes]
rs9839082	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9844741	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs9850125	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9851485	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9855716	0.82[JPT][hapmap]
rs9857606	0.89[CHB][hapmap];0.87[CHD][hapmap];0.89[GIH][hapmap];0.85[JPT][hapmap];0.88[ASN][1000 genomes]
rs9861713	0.90[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs9871451	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9871598	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9917755	0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:13 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2759152	chr3:60781943-61220809	Enhancers Weak transcription Active TSS ZNF genes & repeats Flanking Active TSS Strong transcription Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv948633	chr3:60993915-61171279	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv2757873	chr3:61019003-61185558	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	nsv876866	chr3:61054494-61310328	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
5	nsv876867	chr3:61054494-61474575	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
6	nsv432423	chr3:61100255-61606060	Enhancers Active TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
7	nsv1000378	chr3:61103229-61238089	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
8	nsv590425	chr3:61132698-61186550	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	nsv1012435	chr3:61136874-61181318	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv1014142	chr3:61136874-61184782	Weak transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv2756994	chr3:61144427-61220809	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv876868	chr3:61145050-61282503	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
13	nsv527725	chr3:61158423-61160226	Enhancers Weak transcription Flanking Active TSS	n/a	n/a	inside rSNPs	diseases

No data

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:61151200-61188000	Weak transcription	Primary T cells from cord blood	blood
2	chr3:61154200-61160400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr3:61157200-61160000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr3:61157400-61159600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr3:61157400-61161200	Enhancers	Primary hematopoietic stem cells short term culture	blood
6	chr3:61157600-61161000	Enhancers	Primary hematopoietic stem cells	blood
7	chr3:61158000-61159600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr3:61158800-61160200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
9	chr3:61158800-61160600	Weak transcription	HUES64 Cell Line	embryonic stem cell
10	chr3:61158800-61172000	Weak transcription	Pancreas	Pancrea
11	chr3:61159000-61159600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:61159000-61159800	Enhancers	Fetal Heart	heart
13	chr3:61159200-61160000	Enhancers	HepG2	liver
14	chr3:61159400-61159600	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr3:61159400-61159600	Enhancers	Gastric	stomach
16	chr3:61159400-61159800	Enhancers	Liver	Liver
17	chr3:61159400-61160000	Enhancers	Fetal Intestine Large	intestine
18	chr3:61159400-61163400	Weak transcription	Brain Substantia Nigra	brain

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