Variant report

Variant	rs2296960
Chromosome Location	chr1:179514777-179514778
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:179510162..179512565-chr1:179513904..179515636,2	K562	blood:
2	chr1:179510162..179513711-chr1:179513904..179516885,3	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-NPHS2-1	chr1:179512336-179515388	ENSG00000261250.1

Extended variants
information (count: 85 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:84)

rs_ID	r²[population]
rs10494517	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10494518	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10913765	0.84[CHB][hapmap]
rs10913815	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs11577538	0.83[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11581470	0.87[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap]
rs11584680	0.81[EUR][1000 genomes]
rs11585517	1.00[CEU][hapmap];0.82[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.99[EUR][1000 genomes]
rs11586725	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11808258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12566954	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12743373	0.84[CHB][hapmap]
rs12749731	0.83[CHB][hapmap]
rs12757065	0.84[CHB][hapmap]
rs13306732	0.84[CEU][hapmap]
rs1410585	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1410587	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs1410588	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs16854042	0.87[CEU][hapmap];0.93[CHB][hapmap];0.90[JPT][hapmap]
rs16854244	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2149399	0.89[CHB][hapmap];0.82[ASN][1000 genomes]
rs2209922	1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.84[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs2274622	0.81[JPT][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs2274626	0.83[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs3754132	0.89[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs3765547	0.81[JPT][hapmap];1.00[YRI][hapmap]
rs4072451	0.88[CEU][hapmap];0.94[CHB][hapmap]
rs4072452	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs4111171	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[JPT][hapmap];0.88[YRI][hapmap];0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs41267596	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4400577	0.84[CHB][hapmap]
rs4424468	0.84[CHB][hapmap]
rs4651025	0.84[CHB][hapmap]
rs4651041	0.90[EUR][1000 genomes]
rs4651042	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652369	0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4652374	0.84[CHB][hapmap]
rs4652380	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs4652400	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4652406	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652407	0.81[AFR][1000 genomes];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4652408	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4652411	0.91[EUR][1000 genomes]
rs4652412	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs55908143	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs56071531	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56237305	0.91[EUR][1000 genomes]
rs57340322	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6425557	0.87[CEU][hapmap];0.94[CHB][hapmap];0.80[JPT][hapmap]
rs6425571	0.91[EUR][1000 genomes]
rs6425572	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6425574	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.88[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6657452	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6658180	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6662262	0.83[JPT][hapmap];0.84[ASN][1000 genomes]
rs6664339	0.83[CHB][hapmap]
rs6666455	0.87[CEU][hapmap]
rs6666456	0.88[YRI][hapmap]
rs6668120	1.00[CEU][hapmap];0.88[YRI][hapmap]
rs6674086	1.00[CEU][hapmap];0.87[YRI][hapmap]
rs6678667	0.84[CHB][hapmap]
rs6679542	0.91[JPT][hapmap]
rs6690348	0.84[CHB][hapmap]
rs6693627	0.84[CHB][hapmap]
rs6700149	0.88[CEU][hapmap];0.95[CHB][hapmap];0.81[JPT][hapmap]
rs72704417	0.81[EUR][1000 genomes]
rs72704467	0.90[EUR][1000 genomes]
rs72704477	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7413415	0.88[CEU][hapmap];0.95[CHB][hapmap];0.82[JPT][hapmap]
rs7512638	1.00[CEU][hapmap];0.88[YRI][hapmap];0.90[EUR][1000 genomes]
rs7519700	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7520806	0.80[CEU][hapmap]
rs7529107	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7541890	0.84[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7541899	0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs7548654	0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7551440	0.89[CHB][hapmap]
rs7551610	0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs913514	0.91[JPT][hapmap]
rs928017	0.82[JPT][hapmap];0.84[ASN][1000 genomes]
rs9286930	0.93[ASN][1000 genomes]
rs962428	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs964983	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs964984	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[YRI][hapmap];0.81[AFR][1000 genomes];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv522746	chr1:179501365-179518459	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2296960	TDRD5	cis	Thyroid	GTEx
rs2296960	RP11-545A16.3	cis	Artery Aorta	GTEx
rs2296960	TDRD5	cis	Artery Tibial	GTEx
rs2296960	TDRD5	cis	Skin Sun Exposed Lower leg	GTEx
rs2296960	TDRD5	cis	Nerve Tibial	GTEx
rs2296960	TDRD5	cis	Esophagus Mucosa	GTEx
rs2296960	TDRD5	cis	Adipose Subcutaneous	GTEx
rs2296960	TDRD5	cis	Artery Aorta	GTEx

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179487200-179515000	Weak transcription	Rectal Mucosa Donor 31	rectum
2	chr1:179510600-179520600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:179514000-179518200	Enhancers	Breast Myoepithelial Primary Cells	Breast
4	chr1:179514400-179515400	Enhancers	Fetal Muscle Leg	muscle
5	chr1:179514400-179515600	Weak transcription	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links