Variant report

Variant	rs4234398
Chromosome Location	chr3:110399313-110399314
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 116 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:104)

rs_ID	r²[population]
rs10934065	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1156330	0.88[EUR][1000 genomes]
rs1156743	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156744	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1156775	0.88[EUR][1000 genomes]
rs1156776	0.87[EUR][1000 genomes]
rs1156777	0.88[EUR][1000 genomes]
rs11715183	0.82[EUR][1000 genomes]
rs11721105	0.85[ASN][1000 genomes]
rs1303902	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13077386	0.89[MEX][hapmap]
rs13098266	0.84[EUR][1000 genomes]
rs13098277	0.84[EUR][1000 genomes]
rs1350929	0.88[EUR][1000 genomes]
rs1381604	0.80[EUR][1000 genomes]
rs1462294	0.87[EUR][1000 genomes]
rs1462301	0.80[EUR][1000 genomes]
rs1462302	0.88[EUR][1000 genomes]
rs1462303	0.87[EUR][1000 genomes]
rs1462306	0.87[EUR][1000 genomes]
rs1462314	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1462315	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1462316	0.87[EUR][1000 genomes]
rs1473828	0.84[EUR][1000 genomes]
rs1547543	0.84[EUR][1000 genomes]
rs1585559	0.81[EUR][1000 genomes]
rs1599569	0.86[EUR][1000 genomes]
rs1599570	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1599572	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1599574	0.82[EUR][1000 genomes]
rs17202466	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1824630	0.89[EUR][1000 genomes]
rs1903678	0.88[EUR][1000 genomes]
rs2054375	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2126450	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2169496	0.81[EUR][1000 genomes]
rs2199454	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2399356	0.88[EUR][1000 genomes]
rs2399357	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2399361	0.88[EUR][1000 genomes]
rs4234400	0.90[EUR][1000 genomes]
rs4362750	0.90[EUR][1000 genomes]
rs4395426	0.84[EUR][1000 genomes]
rs4410465	0.84[EUR][1000 genomes]
rs4438690	0.88[EUR][1000 genomes]
rs4449350	0.84[EUR][1000 genomes]
rs4450854	0.84[EUR][1000 genomes]
rs4469006	0.83[EUR][1000 genomes]
rs4481181	0.90[EUR][1000 genomes]
rs4547734	0.84[EUR][1000 genomes]
rs4550849	0.84[EUR][1000 genomes]
rs4588395	0.83[EUR][1000 genomes]
rs4634158	0.84[EUR][1000 genomes]
rs4640600	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4682014	0.84[EUR][1000 genomes]
rs4682018	0.91[EUR][1000 genomes]
rs4682019	0.81[EUR][1000 genomes]
rs4682020	0.83[EUR][1000 genomes]
rs4682192	0.84[EUR][1000 genomes]
rs4682193	0.84[EUR][1000 genomes]
rs4682194	0.84[EUR][1000 genomes]
rs4682195	0.84[EUR][1000 genomes]
rs4682198	0.91[EUR][1000 genomes]
rs4682204	0.81[EUR][1000 genomes]
rs55894328	0.87[EUR][1000 genomes]
rs56203101	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6437925	0.88[EUR][1000 genomes]
rs6762150	0.88[EUR][1000 genomes]
rs6773268	0.83[EUR][1000 genomes]
rs6784490	0.90[EUR][1000 genomes]
rs6809227	0.89[EUR][1000 genomes]
rs7615772	0.88[EUR][1000 genomes]
rs7629191	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7633076	0.88[EUR][1000 genomes]
rs7633936	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.94[JPT][hapmap];0.89[MEX][hapmap];0.96[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7637105	0.83[EUR][1000 genomes]
rs7637286	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7640594	0.88[EUR][1000 genomes]
rs7647181	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7647421	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs931019	0.83[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs9816253	0.88[EUR][1000 genomes]
rs9820478	0.88[EUR][1000 genomes]
rs9826294	0.84[EUR][1000 genomes]
rs9830854	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9830959	0.88[EUR][1000 genomes]
rs9836371	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9837589	0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9838550	0.91[EUR][1000 genomes]
rs9838611	0.84[EUR][1000 genomes]
rs9838715	0.82[EUR][1000 genomes]
rs9840671	0.84[EUR][1000 genomes]
rs9842924	0.88[EUR][1000 genomes]
rs9843528	0.83[EUR][1000 genomes]
rs9843978	0.84[EUR][1000 genomes]
rs9844791	0.84[EUR][1000 genomes]
rs9857065	0.82[EUR][1000 genomes]
rs9857228	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9863549	0.84[EUR][1000 genomes]
rs9864306	0.82[EUR][1000 genomes]
rs9876058	0.84[EUR][1000 genomes]
rs9884058	0.84[EUR][1000 genomes]
rs991930	0.82[EUR][1000 genomes]
rs994125	0.88[EUR][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	nsv520365	chr3:110155172-110441165	Weak transcription Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv1001144	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
3	nsv536687	chr3:110158316-110431113	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
4	nsv1001810	chr3:110158316-110522247	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
5	nsv1010230	chr3:110204439-110588814	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
6	nsv536688	chr3:110204439-110588814	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv1011034	chr3:110209344-110559021	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
8	nsv536689	chr3:110209344-110559021	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
9	nsv1003106	chr3:110264476-111105943	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
10	nsv1014199	chr3:110293896-110754155	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
11	nsv829673	chr3:110378069-110530815	Enhancers Weak transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
12	nsv3941	chr3:110385790-110430523	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:110397000-110402600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr3:110398400-110402600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
3	chr3:110398400-110402800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:110398400-110404600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr3:110398600-110400000	Enhancers	Fetal Brain Male	brain
6	chr3:110398600-110403000	Weak transcription	Fetal Lung	lung

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