Variant report

Variant	rs4679631
Chromosome Location	chr3:60091156-60091157
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs13060068	1.00[CHB][hapmap]
rs17061972	1.00[CHB][hapmap]
rs17257269	1.00[CHB][hapmap]
rs212010	1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs212036	1.00[CHB][hapmap]
rs212038	1.00[CHB][hapmap]
rs2223085	0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2361336	1.00[JPT][hapmap]
rs2361337	1.00[CEU][hapmap]
rs2366953	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2630165	1.00[CHB][hapmap];1.00[ASN][1000 genomes]
rs2630182	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2630195	1.00[ASN][1000 genomes]
rs2630205	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2736763	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2736776	1.00[ASN][1000 genomes]
rs2736820	1.00[ASN][1000 genomes]
rs34267930	0.89[ASN][1000 genomes]
rs3845974	1.00[CHB][hapmap]
rs4024129	1.00[JPT][hapmap]
rs4679510	0.82[EUR][1000 genomes]
rs4679629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4679636	1.00[CEU][hapmap];1.00[JPT][hapmap]
rs6446109	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6446110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67136973	0.89[ASN][1000 genomes]
rs6773600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6782148	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6789112	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes]
rs6791450	1.00[JPT][hapmap]
rs6794055	1.00[JPT][hapmap]
rs6797474	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6798836	0.87[EUR][1000 genomes]
rs6804216	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6806074	1.00[JPT][hapmap]
rs7609578	1.00[JPT][hapmap]
rs7642268	1.00[JPT][hapmap]
rs9311748	0.89[ASN][1000 genomes]
rs969562	1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9833389	0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs986651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:22 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1014983	chr3:59884024-60558331	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
2	nsv590387	chr3:59890976-60481459	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
3	nsv834707	chr3:60005679-60184046	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
4	esv2752010	chr3:60067396-60288428	Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	nsv1009063	chr3:60067866-60277128	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
6	nsv1013919	chr3:60067866-60284882	Flanking Active TSS Enhancers Weak transcription ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv519855	chr3:60068730-60276722	Weak transcription Enhancers Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
8	nsv460566	chr3:60068730-60276722	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
9	nsv460567	chr3:60068730-60276722	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
10	nsv590390	chr3:60068730-60276722	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
11	nsv590391	chr3:60068730-60277709	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
12	nsv1008586	chr3:60070974-60258108	Weak transcription Enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
13	nsv536576	chr3:60070974-60258108	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
14	nsv1009971	chr3:60070974-60397331	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
15	nsv1008267	chr3:60071947-60264461	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
16	nsv1007798	chr3:60071947-60277128	Enhancers ZNF genes & repeats Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
17	esv2763751	chr3:60071959-60292312	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
18	esv2752011	chr3:60073153-60288428	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
19	nsv432421	chr3:60073153-60288428	Weak transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
20	nsv876840	chr3:60083293-60194570	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
21	nsv529602	chr3:60088353-60830769	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
22	nsv915646	chr3:60088475-60240653	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:60086200-60091600	Enhancers	Fetal Intestine Small	intestine
2	chr3:60088800-60091200	Enhancers	Dnd41	blood
3	chr3:60088800-60091400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
4	chr3:60089600-60091200	Enhancers	Primary T cells from cord blood	blood
5	chr3:60089600-60091800	Enhancers	Primary T helper cells PMA-I stimulated	--
6	chr3:60089600-60092000	Enhancers	Primary T helper cells fromperipheralblood	blood
7	chr3:60089800-60091400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr3:60089800-60091400	Enhancers	Cortex derived primary cultured neurospheres	brain
9	chr3:60089800-60091400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr3:60090000-60091200	Enhancers	Primary T helper naive cells from peripheral blood	blood
11	chr3:60090000-60091400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:60090400-60091200	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr3:60090400-60091200	Enhancers	Primary T regulatory cells fromperipheralblood	blood
14	chr3:60090600-60091200	Enhancers	Brain Substantia Nigra	brain
15	chr3:60090800-60091200	Enhancers	Brain Cingulate Gyrus	brain
16	chr3:60090800-60091200	Enhancers	Brain Hippocampus Middle	brain
17	chr3:60090800-60091400	Enhancers	Brain Angular Gyrus	brain
18	chr3:60091000-60091400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
19	chr3:60091000-60091800	Weak transcription	Fetal Intestine Large	intestine

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