Variant report

Variant	rs1249804
Chromosome Location	chr1:75840934-75840935
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 18 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs1249808	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249809	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249810	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249812	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249813	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249818	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249819	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249846	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1313031	0.94[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1313032	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6593573	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3368999	chr1:75524762-75933220	Bivalent/Poised TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1013952	chr1:75716654-75936048	Weak transcription Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	nsv535004	chr1:75716654-75936048	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1455	chr1:75812377-75864182	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
5	nsv519329	chr1:75830438-76358591	Enhancers Strong transcription Flanking Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
6	nsv508304	chr1:75838772-75857426	Active TSS Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases
7	nsv435643	chr1:75840855-75848976	Active TSS Weak transcription Flanking Active TSS Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1249804	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:75831200-75841000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:75831400-75841400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr1:75833400-75841000	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr1:75833600-75841200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr1:75836800-75841200	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr1:75837800-75841600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr1:75838200-75841800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr1:75840000-75841000	Weak transcription	Rectal Mucosa Donor 29	rectum
9	chr1:75840000-75841800	Active TSS	ES-I3 Cell Line	embryonic stem cell
10	chr1:75840200-75841000	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:75840400-75841000	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr1:75840400-75841200	Weak transcription	Placenta	Placenta
13	chr1:75840400-75841600	Active TSS	HepG2	liver
14	chr1:75840600-75841000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell
15	chr1:75840600-75841600	Active TSS	K562	blood
16	chr1:75840600-75841600	Active TSS	NHEK	skin
17	chr1:75840600-75842000	Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr1:75840800-75841000	Enhancers	HUES48 Cell Line	embryonic stem cell
19	chr1:75840800-75841200	Flanking Active TSS	HUES64 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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