Variant report

Variant	rs1607680
Chromosome Location	chr3:102406773-102406774
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs1158525	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1391421	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1391425	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1474185	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1498085	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1520171	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1520172	0.82[ASW][hapmap];1.00[LWK][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1599775	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1599777	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1607684	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1715543	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1715550	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs1818701	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs6765815	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7614607	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs7624014	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs939327	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs973692	0.91[AFR][1000 genomes];1.00[AMR][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	nsv1007340	chr3:102108954-102725099	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
2	nsv536676	chr3:102108954-102725099	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	nsv1009392	chr3:102199756-102631205	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
4	nsv877228	chr3:102345638-102751470	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv591190	chr3:102345638-102946216	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
6	nsv834776	chr3:102351486-102532042	Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
7	nsv1000584	chr3:102358773-102923378	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer ZNF genes & repeats Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
8	nsv915978	chr3:102386795-102949530	Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:102404800-102407600	Enhancers	iPS-18 Cell Line	embryonic stem cell
2	chr3:102404800-102407800	Enhancers	HUES64 Cell Line	embryonic stem cell
3	chr3:102405400-102406800	Enhancers	H1 Cell Line	embryonic stem cell
4	chr3:102405400-102407200	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:102405400-102408800	Enhancers	iPS-15b Cell Line	embryonic stem cell
6	chr3:102405600-102406800	Enhancers	H9 Cell Line	embryonic stem cell
7	chr3:102405600-102407000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr3:102405600-102407400	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr3:102406200-102406800	Enhancers	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr3:102406200-102406800	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
11	chr3:102406200-102407000	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:102406400-102406800	Flanking Active TSS	HUES48 Cell Line	embryonic stem cell
13	chr3:102406400-102406800	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr3:102406400-102407000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
15	chr3:102406600-102406800	Flanking Active TSS	HUES6 Cell Line	embryonic stem cell
16	chr3:102406600-102414800	Weak transcription	Fetal Heart	heart

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

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