Variant report

Variant	rs2793661
Chromosome Location	chr1:56724405-56724406
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	CTCF	chr1:56724274-56724411	GM12878	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000260971	TF binding region

Extended variants
information (count: 33 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs1119073	0.88[CHB][hapmap]
rs11206749	0.86[EUR][1000 genomes]
rs11206750	0.85[EUR][1000 genomes]
rs12136560	0.80[ASN][1000 genomes]
rs12564025	0.97[ASN][1000 genomes]
rs1331862	0.85[EUR][1000 genomes]
rs1360504	0.83[EUR][1000 genomes]
rs1417770	0.97[ASN][1000 genomes]
rs17113557	0.81[ASN][1000 genomes]
rs1935050	0.86[JPT][hapmap]
rs2777758	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2792774	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2792775	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2792776	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2792794	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2792795	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793660	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2793662	0.86[JPT][hapmap]
rs2793663	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793664	0.91[CEU][hapmap];0.90[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2793665	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793666	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2793677	0.82[EUR][1000 genomes]
rs2793688	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs2793691	0.81[EUR][1000 genomes]
rs706402	0.86[EUR][1000 genomes]
rs72675574	0.85[EUR][1000 genomes]
rs7512969	0.80[ASN][1000 genomes]
rs9436537	0.85[AMR][1000 genomes]
rs9436538	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9436999	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs947007	0.80[JPT][hapmap]
rs947008	0.80[JPT][hapmap]

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs2793661	TTC4	cis	cerebellum	SCAN
rs2793661	HSPB11	cis	parietal	SCAN
rs2793661	QPCT	trans	lymphoblastoid	seeQTL

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:56720800-56725200	Enhancers	Fetal Muscle Leg	muscle
2	chr1:56720800-56725400	Enhancers	Skeletal Muscle Male	skeletal muscle
3	chr1:56721200-56725000	Enhancers	Psoas Muscle	Psoas
4	chr1:56721800-56725000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr1:56721800-56730000	Weak transcription	Ovary	ovary
6	chr1:56722200-56725000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
7	chr1:56722200-56725000	Weak transcription	Fetal Heart	heart
8	chr1:56722800-56726000	Weak transcription	Colon Smooth Muscle	Colon
9	chr1:56723600-56724800	Enhancers	Fetal Thymus	thymus
10	chr1:56723600-56725000	Enhancers	Stomach Smooth Muscle	stomach
11	chr1:56723600-56725600	Enhancers	Left Ventricle	heart
12	chr1:56723800-56725000	Enhancers	Brain Anterior Caudate	brain
13	chr1:56723800-56725200	Enhancers	Brain Cingulate Gyrus	brain
14	chr1:56724000-56724800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr1:56724000-56725000	Enhancers	Brain Inferior Temporal Lobe	brain
16	chr1:56724200-56724600	Enhancers	Brain Substantia Nigra	brain
17	chr1:56724200-56726000	Weak transcription	Placenta	Placenta
18	chr1:56724400-56725000	Enhancers	iPS-18 Cell Line	embryonic stem cell
19	chr1:56724400-56725000	Weak transcription	Right Atrium	heart
20	chr1:56724400-56725600	Enhancers	Skeletal Muscle Female	skeletal muscle

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