Variant report

Variant	rs2421987
Chromosome Location	chr1:172100831-172100832
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10442603	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[YRI][hapmap];0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10797736	0.91[CHB][hapmap];0.80[ASN][1000 genomes]
rs10797791	1.00[CEU][hapmap];0.86[CHD][hapmap];0.85[GIH][hapmap];0.95[JPT][hapmap];0.91[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10910945	1.00[CHB][hapmap];0.80[JPT][hapmap]
rs10911101	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10911109	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs10911110	1.00[CEU][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911111	0.88[CEU][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10911112	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs10911116	1.00[CEU][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs10911121	0.94[CEU][hapmap]
rs10911124	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.82[MEX][hapmap];0.81[AMR][1000 genomes]
rs10911125	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap]
rs12047492	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs12117623	0.82[ASN][1000 genomes]
rs12119190	1.00[CHB][hapmap];0.88[CHD][hapmap];0.82[JPT][hapmap];0.87[MEX][hapmap];0.84[ASN][1000 genomes]
rs12120556	1.00[CEU][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes]
rs12139213	0.84[ASN][1000 genomes]
rs12141278	0.93[AMR][1000 genomes];0.99[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1475230	0.94[CEU][hapmap];0.84[CHD][hapmap];0.90[JPT][hapmap];0.86[MEX][hapmap]
rs1475231	0.94[CEU][hapmap];0.90[JPT][hapmap]
rs2146901	1.00[CEU][hapmap];0.86[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.94[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2181624	1.00[CEU][hapmap];0.88[TSI][hapmap];0.95[EUR][1000 genomes]
rs2421986	0.96[EUR][1000 genomes]
rs4604727	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.85[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs59123063	0.81[AMR][1000 genomes]
rs6413836	0.82[ASN][1000 genomes]
rs72719073	0.83[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs72719075	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs72719086	0.81[AMR][1000 genomes]
rs7519823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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	nsv532342	chr1:171922237-172133785	Weak transcription Flanking Active TSS Enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	62 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2421987	TNFSF18	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172049400-172110800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr1:172062400-172109200	Weak transcription	Brain Cingulate Gyrus	brain
3	chr1:172069200-172102000	Weak transcription	Brain Hippocampus Middle	brain
4	chr1:172077200-172110600	Weak transcription	Brain Angular Gyrus	brain
5	chr1:172085800-172113400	Weak transcription	Pancreas	Pancrea
6	chr1:172090000-172109600	Weak transcription	Brain Germinal Matrix	brain
7	chr1:172090400-172108800	Weak transcription	Fetal Stomach	stomach
8	chr1:172090800-172102200	Weak transcription	Brain Inferior Temporal Lobe	brain
9	chr1:172092000-172102800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr1:172094600-172110600	Weak transcription	Left Ventricle	heart
11	chr1:172095400-172102000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr1:172096000-172103200	Weak transcription	Gastric	stomach
13	chr1:172096400-172110600	Weak transcription	Brain Substantia Nigra	brain
14	chr1:172097600-172101600	Weak transcription	Brain Anterior Caudate	brain
15	chr1:172097600-172102000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr1:172100200-172108600	Weak transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links