Variant report

Variant	rs1249810
Chromosome Location	chr1:75834454-75834455
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 10 )

rSNPs within LD-proxies of this variant (count:17)

rs_ID	r²[population]
rs10874314	0.89[JPT][hapmap]
rs1249804	0.97[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249808	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.96[MKK][hapmap];0.97[TSI][hapmap];0.94[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249809	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249811	0.90[MKK][hapmap]
rs1249812	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249813	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.80[LWK][hapmap];0.80[MKK][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249815	0.91[MKK][hapmap]
rs1249818	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249819	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249846	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1249849	0.90[MKK][hapmap]
rs1313031	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs1313032	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1867352	1.00[JPT][hapmap]
rs1889037	1.00[JPT][hapmap]
rs6593573	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs1249810	SLC44A5	cis	lung	GTEx
rs1249810	SLC44A5	cis	Esophagus Mucosa	GTEx
rs1249810	SLC44A5	cis	uninvolved skin	skin_eQTL
rs1249810	SLC44A5	cis	lesional skin	skin_eQTL
rs1249810	SLC44A5	cis	Muscle Skeletal	GTEx
rs1249810	SLC44A5	cis	Heart Left Ventricle	GTEx
rs1249810	SLC44A5	Cis_1M	lymphoblastoid	RTeQTL
rs1249810	SLC44A5	cis	normal skin	skin_eQTL
rs1249810	SLC44A5	cis	Skin Sun Exposed Lower leg	GTEx
rs1249810	SLC44A5	cis	Thyroid	GTEx

Chromatin state (count:11 , 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	chr1:75833200-75836200	Weak transcription	HUES64 Cell Line	embryonic stem cell
4	chr1:75833400-75837000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr1:75833400-75839200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr1:75833400-75839200	Weak transcription	K562	blood
7	chr1:75833400-75841000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr1:75833600-75837600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr1:75833600-75839200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
10	chr1:75833600-75841200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr1:75834400-75838200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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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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