Variant report

Variant	rs2588393
Chromosome Location	chr12:40884061-40884062
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:40882994..40885029-chr12:40904694..40907438,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-MUC19-1	chr12:40879237-40885130	NONHSAT027728

Extended variants
information (count: 54 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1444214	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1444217	0.92[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1444222	0.92[AFR][1000 genomes];0.84[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1492313	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs1492322	0.92[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1826383	0.82[AFR][1000 genomes]
rs1838351	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.80[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2452314	0.88[AFR][1000 genomes]
rs2452315	0.88[AFR][1000 genomes]
rs2588394	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2588401	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2588402	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2588411	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638862	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638863	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638864	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638865	0.93[AFR][1000 genomes];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2638867	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2638869	0.93[AFR][1000 genomes];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638875	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2638883	0.92[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2920827	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2933355	0.93[AFR][1000 genomes];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2933356	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2933367	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2933373	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2933376	0.95[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs719227	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs719228	0.97[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:25 , 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	esv1827225	chr12:40873026-40894172	Weak transcription ZNF genes & repeats Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
6	esv1833623	chr12:40873026-40894172	ZNF genes & repeats Weak transcription Strong transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
7	nsv821471	chr12:40873057-40885132	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
8	esv16680	chr12:40873057-40885157	ZNF genes & repeats Strong transcription Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
9	esv1834493	chr12:40874860-40884744	ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
10	nsv558635	chr12:40874912-40884881	ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
11	nsv558645	chr12:40875014-40884744	ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
12	nsv558663	chr12:40875303-40884881	ZNF genes & repeats Weak transcription	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
13	nsv558669	chr12:40875351-40884744	Weak transcription ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
14	nsv558691	chr12:40876644-40884403	ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
15	nsv558693	chr12:40877007-40884403	ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
16	nsv8969	chr12:40877065-40884382	ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
17	esv2427709	chr12:40877987-40884242	ZNF genes & repeats	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
18	nsv558695	chr12:40879177-40884403	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
19	nsv437747	chr12:40880060-40884666	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
20	nsv437748	chr12:40880060-40884666	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
21	nsv437749	chr12:40880060-40884666	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
22	nsv437750	chr12:40880060-40884666	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
23	esv3372529	chr12:40880885-40885083	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
24	esv996769	chr12:40881764-40886597	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases
25	esv3445765	chr12:40883611-40884468	Inactive region	Chromatin interactive region lncRNA	n/a	inside rSNPs	diseases

No data

Chromatin state (count:0 , 50 per page) page:

No data

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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