Variant report

Variant	rs2972076
Chromosome Location	chr2:55288803-55288804
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:55287127..55289595-chr2:55348601..55351225,2	K562	blood:
2	chr2:55288774..55290302-chr2:55293407..55295597,2	K562	blood:
3	chr2:55287997..55290069-chr2:55324008..55326423,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10179594	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10196667	0.82[CEU][hapmap]
rs10205017	0.90[EUR][1000 genomes]
rs10746530	0.82[CEU][hapmap]
rs11125551	0.82[CEU][hapmap]
rs12989576	0.82[CEU][hapmap];0.85[JPT][hapmap];0.93[EUR][1000 genomes]
rs13002841	0.82[CEU][hapmap];0.90[EUR][1000 genomes]
rs13023202	0.91[EUR][1000 genomes]
rs2580763	0.85[JPT][hapmap];0.87[EUR][1000 genomes]
rs2580766	0.82[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs2588520	0.82[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs2919125	0.82[CEU][hapmap];0.85[JPT][hapmap];0.91[EUR][1000 genomes]
rs2920839	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2920861	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920863	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[EUR][1000 genomes]
rs2920872	0.81[ASN][1000 genomes]
rs2920881	1.00[CHB][hapmap];0.93[JPT][hapmap];0.83[ASN][1000 genomes]
rs2920883	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920884	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920889	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920890	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920897	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2920898	0.85[CHB][hapmap];0.85[JPT][hapmap]
rs2968789	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2968792	0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2968810	0.81[ASN][1000 genomes]
rs2968812	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2968813	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2968814	1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs2968823	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968824	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968826	0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2968829	1.00[CHB][hapmap];0.93[JPT][hapmap];0.86[ASN][1000 genomes]
rs2968831	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2972065	0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972066	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2972067	0.83[ASN][1000 genomes]
rs2972069	0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2972073	0.83[ASN][1000 genomes]
rs2972074	0.81[ASN][1000 genomes]
rs3099068	0.83[ASN][1000 genomes]
rs6545462	0.82[CEU][hapmap]
rs7559248	0.97[EUR][1000 genomes];0.98[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	nsv874155	chr2:55205262-55307646	Weak transcription Enhancers Flanking Active TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	37 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2972076	RTN4	cis	Thyroid	GTEx

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55278800-55290800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr2:55279000-55290600	Weak transcription	Brain Cingulate Gyrus	brain
3	chr2:55280000-55289000	Weak transcription	HepG2	liver
4	chr2:55287800-55292200	Weak transcription	Fetal Heart	heart
5	chr2:55288000-55290400	Weak transcription	K562	blood
6	chr2:55288200-55289600	Enhancers	Primary monocytes fromperipheralblood	blood
7	chr2:55288400-55289400	Enhancers	Monocytes-CD14+_RO01746	blood
8	chr2:55288800-55289600	Enhancers	Lung	lung

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