Variant report

Variant	rs483259
Chromosome Location	chr1:74710629-74710630
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 72 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:60)

rs_ID	r²[population]
rs10789391	0.97[ASN][1000 genomes]
rs10890119	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11210431	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11210434	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs11210440	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11210441	0.98[ASN][1000 genomes]
rs11210442	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11806946	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs12134868	0.88[ASN][1000 genomes]
rs12142236	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs1412824	0.97[ASN][1000 genomes]
rs1412825	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs35920753	0.87[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs3765651	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4422957	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs4650251	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs474215	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs476350	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs477134	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs481387	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs485929	0.97[ASN][1000 genomes]
rs487917	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs488813	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs489941	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs491623	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs492302	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs495027	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs496008	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs500203	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs504866	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs520806	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs522042	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs522759	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs524306	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs526736	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs531412	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532221	1.00[ASN][1000 genomes]
rs533371	0.89[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs536355	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs539534	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs542136	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs545664	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs545680	0.85[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs545721	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs553044	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs560808	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs567060	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs568049	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs571848	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs577367	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs581353	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs61778032	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7535418	0.97[ASN][1000 genomes]
rs792307	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs792310	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs792321	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs813192	0.81[AMR][1000 genomes];0.90[ASN][1000 genomes]
rs9425023	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs944795	0.84[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs956	0.85[AMR][1000 genomes];0.97[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:12 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1004451	chr1:74107125-74874389	Enhancers Active TSS Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
2	nsv534999	chr1:74107125-74874389	Weak transcription Enhancers ZNF genes & repeats Genic enhancers Active TSS Strong transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
3	nsv522147	chr1:74338530-74983835	Active TSS Flanking Active TSS Enhancers Weak transcription Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
4	nsv1003171	chr1:74407468-75122270	Strong transcription Enhancers Bivalent Enhancer Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
5	nsv535000	chr1:74407468-75122270	Enhancers Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
6	nsv871381	chr1:74484753-74712181	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
7	nsv871456	chr1:74492200-74712181	Transcr. at gene 5' and 3' Flanking Active TSS Weak transcription Strong transcription Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
8	nsv1011308	chr1:74545016-74932777	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
9	nsv428785	chr1:74640545-74818577	Active TSS Flanking Active TSS Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
10	nsv870486	chr1:74654182-74804833	Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
11	nsv870554	chr1:74678285-74804833	Enhancers ZNF genes & repeats Weak transcription Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
12	nsv523474	chr1:74699099-74794119	Weak transcription Strong transcription Flanking Bivalent TSS/Enh Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs483259	FPGT	cis	Esophagus Muscularis	GTEx
rs483259	LRRIQ3	cis	Thyroid	GTEx
rs483259	LRRC44	Cis_1M	lymphoblastoid	RTeQTL
rs483259	FPGT	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:74671400-74719400	Weak transcription	Skeletal Muscle Female	skeletal muscle
2	chr1:74671400-74751800	Weak transcription	Ovary	ovary
3	chr1:74675800-74724000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr1:74700600-74713800	Weak transcription	Adipose Nuclei	Adipose
5	chr1:74703800-74716600	Weak transcription	Left Ventricle	heart
6	chr1:74708000-74711000	Enhancers	Fetal Heart	heart
7	chr1:74710000-74712200	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
8	chr1:74710000-74712400	Bivalent Enhancer	HUES64 Cell Line	embryonic stem cell
9	chr1:74710000-74713000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr1:74710200-74712200	Bivalent Enhancer	HUES48 Cell Line	embryonic stem cell
11	chr1:74710400-74711000	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr1:74710400-74711400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
13	chr1:74710400-74711800	Enhancers	HUES6 Cell Line	embryonic stem cell
14	chr1:74710400-74713000	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr1:74710600-74710800	Flanking Bivalent TSS/Enh	iPS-18 Cell Line	embryonic stem cell
16	chr1:74710600-74711000	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links