Variant report

Variant	rs6550953
Chromosome Location	chr3:25199766-25199767
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs2043619	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2043620	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2363595	0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2649616	0.85[ASN][1000 genomes]
rs2885836	0.84[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs321521	0.85[ASN][1000 genomes]
rs321524	0.85[ASN][1000 genomes]
rs321525	0.85[ASN][1000 genomes]
rs321539	0.85[ASN][1000 genomes]
rs321540	0.85[ASN][1000 genomes]
rs321542	0.93[JPT][hapmap]
rs4258924	0.82[AFR][1000 genomes];0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6793141	0.95[AFR][1000 genomes];0.84[ASN][1000 genomes]
rs6796899	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs904593	0.86[AFR][1000 genomes];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs978142	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013446	chr3:25176609-25221334	Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
2	nsv876631	chr3:25185448-25231571	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases
3	nsv949035	chr3:25194301-26084890	Weak transcription Bivalent/Poised TSS Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	68 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:25194000-25211800	Weak transcription	Aorta	Aorta
2	chr3:25196800-25200400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:25197600-25205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:25197800-25200600	Enhancers	ES-I3 Cell Line	embryonic stem cell
5	chr3:25198200-25200600	Enhancers	HUES64 Cell Line	embryonic stem cell
6	chr3:25198400-25199800	Enhancers	iPS-20b Cell Line	embryonic stem cell
7	chr3:25198400-25200000	Enhancers	iPS-15b Cell Line	embryonic stem cell
8	chr3:25198400-25200600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr3:25198400-25200600	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr3:25198600-25201200	Enhancers	iPS-18 Cell Line	embryonic stem cell
11	chr3:25198600-25201200	Weak transcription	Fetal Heart	heart
12	chr3:25198600-25211200	Weak transcription	Fetal Stomach	stomach
13	chr3:25198800-25199800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
14	chr3:25198800-25200000	Enhancers	HUES48 Cell Line	embryonic stem cell
15	chr3:25198800-25200600	Weak transcription	HSMM	muscle
16	chr3:25198800-25207000	Weak transcription	Fetal Lung	lung
17	chr3:25199200-25200400	Weak transcription	H1 Cell Line	embryonic stem cell

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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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