Variant report

Variant	rs1251577
Chromosome Location	chr1:76551813-76551814
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1144345	0.87[ASW][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];0.89[MKK][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1146660	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[TSI][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1146664	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1146665	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11585383	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1251464	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1251576	0.85[YRI][hapmap];0.85[AFR][1000 genomes]
rs1251578	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1335740	1.00[CEU][hapmap];0.82[CHD][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17660501	1.00[CEU][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs17660531	1.00[CEU][hapmap];1.00[GIH][hapmap];0.93[TSI][hapmap];0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2043799	1.00[CEU][hapmap];0.97[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs55811448	0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61771321	0.95[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6683884	0.87[ASN][1000 genomes]
rs6692547	0.94[CEU][hapmap];0.89[EUR][1000 genomes];0.80[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	nsv998499	chr1:76361784-76598712	Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
2	nsv870968	chr1:76490234-76552475	Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Enhancers Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv871862	chr1:76525783-76598209	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1251577	FAM73A	cis	parietal	SCAN

Chromatin state (count:28 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76542200-76553200	Weak transcription	Fetal Intestine Large	intestine
2	chr1:76542800-76572000	Weak transcription	Primary B cells from cord blood	blood
3	chr1:76545600-76552200	Weak transcription	Fetal Intestine Small	intestine
4	chr1:76545600-76558200	Weak transcription	Left Ventricle	heart
5	chr1:76547400-76552200	Weak transcription	Fetal Kidney	kidney
6	chr1:76548000-76561800	Weak transcription	Fetal Brain Female	brain
7	chr1:76548400-76576200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr1:76549000-76552400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr1:76549000-76556200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr1:76549000-76556400	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr1:76549200-76552800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:76549200-76556600	Weak transcription	Brain Anterior Caudate	brain
13	chr1:76549200-76556800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr1:76550000-76556600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr1:76550200-76556800	Weak transcription	HUES64 Cell Line	embryonic stem cell
16	chr1:76550400-76552000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
17	chr1:76550400-76552200	Weak transcription	Fetal Stomach	stomach
18	chr1:76550600-76552200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr1:76550800-76552200	Weak transcription	Brain Substantia Nigra	brain
20	chr1:76551200-76552600	Weak transcription	Brain Hippocampus Middle	brain
21	chr1:76551200-76553000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr1:76551200-76556200	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr1:76551400-76554000	Enhancers	Fetal Lung	lung
24	chr1:76551400-76556000	Weak transcription	H1 Cell Line	embryonic stem cell
25	chr1:76551400-76556000	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:76551600-76552400	Weak transcription	Colon Smooth Muscle	Colon
27	chr1:76551600-76552600	Enhancers	HUVEC	blood vessel
28	chr1:76551600-76554400	Enhancers	Stomach Mucosa	stomach

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links