Variant report

Variant	rs2274622
Chromosome Location	chr1:179520050-179520051
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	FOS	chr1:179519934-179520847	MCF10A-Er-Src	breast:	n/a	n/a
2	STAT3	chr1:179519776-179520264	MCF10A-Er-Src	breast:	n/a	n/a
3	NR3C1	chr1:179519920-179520333	A549	lung:	n/a	n/a
4	FOS	chr1:179519967-179520871	MCF10A-Er-Src	breast:	n/a	n/a
5	STAT3	chr1:179519918-179520205	MCF10A-Er-Src	breast:	n/a	n/a
6	FOS	chr1:179519924-179520833	MCF10A-Er-Src	breast:	n/a	n/a
7	CEBPB	chr1:179519968-179520271	HepG2	liver:	n/a	n/a
8	FOS	chr1:179519936-179520830	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr1:179519986-179520294	MCF10A-Er-Src	breast:	n/a	n/a
10	NR3C1	chr1:179520006-179520270	A549	lung:	n/a	n/a
11	STAT3	chr1:179519828-179520802	MCF10A-Er-Src	breast:	n/a	n/a
12	CEBPB	chr1:179520025-179520222	IMR90	lung:	n/a	n/a
13	JUND	chr1:179519994-179520267	K562	blood:	n/a	chr1:179520098-179520109
14	STAT3	chr1:179519855-179520261	MCF10A-Er-Src	breast:	n/a	n/a
15	JUN	chr1:179519991-179520235	HepG2	liver:	n/a	chr1:179520135-179520148
16	JUND	chr1:179519964-179520291	HepG2	liver:	n/a	chr1:179520098-179520109

Variant related genes	Relation type
AXDND1	TF binding region
ENSG00000261250	TF binding region

Extended variants
information (count: 73 )
Associated
traits (count: 11 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs10157829	0.81[JPT][hapmap]
rs10494517	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs10494518	0.87[ASW][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]
rs1079291	0.83[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs10798709	0.81[JPT][hapmap]
rs10913863	0.81[JPT][hapmap]
rs11577538	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[JPT][hapmap];0.82[LWK][hapmap];0.92[MKK][hapmap];0.97[TSI][hapmap];0.87[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11578278	0.81[JPT][hapmap]
rs11581470	0.81[JPT][hapmap]
rs11585517	0.86[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.82[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs11586725	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11808258	0.87[ASW][hapmap];0.91[JPT][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap]
rs12021675	0.85[JPT][hapmap]
rs12035247	0.81[JPT][hapmap]
rs12042409	0.81[JPT][hapmap]
rs12564117	0.83[GIH][hapmap]
rs13306732	0.81[JPT][hapmap]
rs1410593	0.86[JPT][hapmap]
rs16854042	0.85[JPT][hapmap]
rs1999068	0.84[EUR][1000 genomes]
rs2209922	0.87[ASW][hapmap];0.91[JPT][hapmap];0.87[MKK][hapmap];0.87[YRI][hapmap]
rs2274626	0.91[GIH][hapmap];0.82[JPT][hapmap];0.90[TSI][hapmap]
rs2296960	0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs3765547	0.89[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.84[MKK][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.81[ASN][1000 genomes]
rs4072098	0.81[JPT][hapmap]
rs4072452	0.81[JPT][hapmap]
rs4111171	0.86[JPT][hapmap];0.87[YRI][hapmap]
rs4408116	0.81[JPT][hapmap]
rs4474210	0.81[JPT][hapmap]
rs4651041	0.85[ASN][1000 genomes]
rs4651045	0.81[JPT][hapmap]
rs4652367	0.83[CHB][hapmap]
rs4652369	0.81[JPT][hapmap]
rs4652380	0.81[JPT][hapmap]
rs4652406	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs4652411	0.87[ASN][1000 genomes]
rs4652412	0.91[JPT][hapmap]
rs4652432	0.81[JPT][hapmap]
rs4652433	0.81[JPT][hapmap]
rs4652434	0.81[JPT][hapmap]
rs4652438	0.81[JPT][hapmap]
rs56237305	0.87[ASN][1000 genomes]
rs6425557	0.81[JPT][hapmap]
rs6425571	0.87[ASN][1000 genomes]
rs6425574	0.91[JPT][hapmap];0.87[YRI][hapmap]
rs6425580	0.81[JPT][hapmap]
rs6425581	0.81[JPT][hapmap]
rs6425585	0.81[JPT][hapmap]
rs6425588	0.81[CHB][hapmap];0.81[JPT][hapmap]
rs6666455	0.85[CHD][hapmap];0.90[JPT][hapmap]
rs6666456	0.87[YRI][hapmap]
rs6668120	0.81[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap]
rs6672701	0.81[GIH][hapmap]
rs6674086	0.87[ASW][hapmap];0.81[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap];0.95[JPT][hapmap];0.91[MKK][hapmap];0.87[YRI][hapmap]
rs6679542	0.81[JPT][hapmap]
rs6689426	0.81[CHB][hapmap];0.82[CHD][hapmap];0.86[JPT][hapmap]
rs6691856	0.80[JPT][hapmap]
rs6692069	0.81[JPT][hapmap]
rs6700149	0.81[JPT][hapmap]
rs72704467	0.84[ASN][1000 genomes]
rs7413415	0.81[JPT][hapmap]
rs744446	0.85[EUR][1000 genomes]
rs7512638	0.87[YRI][hapmap];0.83[ASN][1000 genomes]
rs7519436	0.81[JPT][hapmap]
rs7519700	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7541890	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7541899	0.91[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs7543334	0.85[ASN][1000 genomes]
rs7547484	0.81[JPT][hapmap]
rs7551610	0.85[YRI][hapmap]
rs913514	0.83[EUR][1000 genomes]
rs964983	0.87[ASW][hapmap];0.91[JPT][hapmap];0.90[MKK][hapmap];0.87[YRI][hapmap]
rs964984	0.87[ASW][hapmap];0.91[JPT][hapmap];0.92[MKK][hapmap];0.87[YRI][hapmap]

mRNA abundance (count:11)

SNP	Gene	Cis/trans	Tissue	Source
rs2274622	TDRD5	cis	Adipose Subcutaneous	GTEx
rs2274622	TDRD5	cis	Artery Aorta	GTEx
rs2274622	TDRD5	cis	parietal	SCAN
rs2274622	TDRD5	cis	Nerve Tibial	GTEx
rs2274622	SOAT1	cis	cerebellum	SCAN
rs2274622	TDRD5	cis	Esophagus Mucosa	GTEx
rs2274622	TDRD5	cis	Thyroid	GTEx
rs2274622	TDRD5	cis	cerebellum	SCAN
rs2274622	TDRD5	cis	Artery Tibial	GTEx
rs2274622	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs2274622	TDRD5	cis	lung	GTEx

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr1:179515600-179521800	Enhancers	Placenta	Placenta
3	chr1:179516800-179520200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
4	chr1:179518600-179520400	Weak transcription	Gastric	stomach
5	chr1:179518600-179521200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:179519600-179521000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr1:179519600-179521000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr1:179519600-179521400	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr1:179519800-179520400	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
10	chr1:179519800-179520600	Enhancers	NHDF-Ad	bronchial
11	chr1:179519800-179521400	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:179520000-179520200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr1:179520000-179520200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
14	chr1:179520000-179520800	Enhancers	HSMMtube	muscle
15	chr1:179520000-179521000	Enhancers	ES-I3 Cell Line	embryonic stem cell
16	chr1:179520000-179521000	Enhancers	Hela-S3	cervix
17	chr1:179520000-179521000	Enhancers	NHEK	skin
18	chr1:179520000-179521400	Enhancers	GM12878-XiMat	blood

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