Variant report

Variant	rs1961818
Chromosome Location	chr4:190858783-190858784
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr4:190858706-190858889	SH-SY5Y	brain:	n/a	n/a

Variant related genes	Relation type
FRG1	TF binding region

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10001956	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11132770	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11132771	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11736363	0.86[AMR][1000 genomes]
rs11736387	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12641802	0.83[CEU][hapmap];0.93[JPT][hapmap]
rs12646565	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12646667	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12646672	0.81[EUR][1000 genomes]
rs12649488	0.95[CEU][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12649515	0.81[EUR][1000 genomes]
rs13121836	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13121986	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13133725	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13133958	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13140896	0.83[AFR][1000 genomes]
rs13148101	0.82[EUR][1000 genomes]
rs2037947	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2037948	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2078634	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2411549	0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4145515	0.87[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4145516	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4145517	0.87[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6553396	0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6816856	0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6820684	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6837422	0.92[AFR][1000 genomes];0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7657916	0.88[EUR][1000 genomes]
rs7658339	0.87[EUR][1000 genomes]
rs7668489	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7691161	0.84[EUR][1000 genomes]
rs9992042	0.85[EUR][1000 genomes]
rs9996679	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1961818	AF146191.4	cis	Thyroid	GTEx
rs1961818	AF146191.4	cis	Esophagus Muscularis	GTEx

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:190847600-190860800	Weak transcription	Pancreas	Pancrea
2	chr4:190852200-190861200	Weak transcription	Fetal Intestine Large	intestine
3	chr4:190852400-190860800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr4:190856200-190861200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
5	chr4:190857800-190860800	Weak transcription	Left Ventricle	heart
6	chr4:190857800-190861000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr4:190858000-190861200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
8	chr4:190858400-190860800	Weak transcription	Colon Smooth Muscle	Colon
9	chr4:190858400-190860800	Weak transcription	Gastric	stomach
10	chr4:190858600-190858800	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 2	blood
11	chr4:190858600-190859000	ZNF genes & repeats	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr4:190858600-190859000	ZNF genes & repeats	Brain Anterior Caudate	brain
13	chr4:190858600-190865400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links