Variant report

Variant	rs2638863
Chromosome Location	chr12:40873808-40873809
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40872855-40879178	NONHSAT027728

Extended variants
information (count: 50 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1444214	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1444217	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1444222	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492313	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1492320	0.84[ASN][1000 genomes]
rs1492322	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1826383	0.83[AFR][1000 genomes]
rs1838351	0.89[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2251431	0.84[ASN][1000 genomes]
rs2405077	0.84[ASN][1000 genomes]
rs2452314	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2452315	0.91[AFR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2588393	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2588394	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2588401	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588402	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2588411	1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638862	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2638864	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638865	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2638867	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2638869	0.97[AFR][1000 genomes];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2638875	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2638882	0.90[ASN][1000 genomes]
rs2638883	0.92[AFR][1000 genomes];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2920827	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2933351	0.80[ASN][1000 genomes]
rs2933355	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2933356	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2933367	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2933373	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2933376	0.95[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7139187	0.80[ASN][1000 genomes]
rs719227	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs719228	0.97[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899033	chr12:40758652-41122288	Bivalent/Poised TSS Enhancers Strong transcription Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	esv1848303	chr12:40867011-40887238	Enhancers Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
3	esv1850439	chr12:40867211-40887867	Enhancers ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
4	esv20428	chr12:40867874-40884927	Weak transcription Enhancers ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
5	esv3390786	chr12:40871685-40877783	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
6	esv3500652	chr12:40872785-40877883	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
7	nsv516022	chr12:40873026-40874088	ZNF genes & repeats Weak transcription Strong transcription	lncRNA	n/a	inside rSNPs	diseases
8	esv1827225	chr12:40873026-40894172	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1833623	chr12:40873026-40894172	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv821471	chr12:40873057-40885132	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	esv16680	chr12:40873057-40885157	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	esv1816871	chr12:40873251-40875695	Weak transcription Strong transcription ZNF genes & repeats	lncRNA	n/a	inside rSNPs	diseases
13	nsv511492	chr12:40873251-40876644	Weak transcription ZNF genes & repeats Strong transcription	lncRNA	n/a	inside rSNPs	diseases
14	nsv558607	chr12:40873763-40875983	Strong transcription ZNF genes & repeats Weak transcription	lncRNA	n/a	inside rSNPs	diseases
15	nsv558608	chr12:40873808-40875983	Weak transcription	lncRNA	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2638863	ABCD2	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40873800-40875800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links