Variant report

Variant	rs17489267
Chromosome Location	chr12:40445400-40445401
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	12:40441273-40454218..12:40703633-40711447	GM12878	blood:
2	chr12:40443219..40446244-chr12:40497398..40500179,3	MCF-7	breast:
3	chr12:40445246..40446962-chr12:40448695..40451443,2	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C12orf40-2	chr12:40445389-40445642	l_630_chr12:40444222-40445642_testes

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction
ENSG00000151229	Chromatin interaction

rs_ID	r²[population]
rs12368785	1.00[JPT][hapmap]
rs12368891	1.00[JPT][hapmap]
rs13377779	1.00[AMR][1000 genomes]
rs17442206	1.00[JPT][hapmap]
rs17442297	1.00[JPT][hapmap]
rs17442742	1.00[JPT][hapmap]
rs17442980	1.00[JPT][hapmap]
rs17443178	1.00[JPT][hapmap]
rs17443185	1.00[JPT][hapmap]
rs17443206	1.00[JPT][hapmap]
rs17443366	1.00[JPT][hapmap]
rs17443380	1.00[JPT][hapmap]
rs17443387	1.00[JPT][hapmap]
rs17458093	1.00[JPT][hapmap]
rs17458121	1.00[JPT][hapmap]
rs17458202	1.00[JPT][hapmap]
rs17458396	1.00[JPT][hapmap]
rs17458417	1.00[JPT][hapmap]
rs17458487	1.00[JPT][hapmap]
rs17458528	1.00[JPT][hapmap]
rs17458836	1.00[JPT][hapmap]
rs17461337	1.00[JPT][hapmap]
rs17465737	1.00[JPT][hapmap]
rs17465751	1.00[JPT][hapmap]
rs17483857	1.00[JPT][hapmap]
rs17483996	1.00[JPT][hapmap]
rs17489170	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17489218	1.00[JPT][hapmap]
rs17489225	1.00[JPT][hapmap]
rs17489246	1.00[JPT][hapmap]
rs17489253	1.00[JPT][hapmap]
rs17489295	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489309	0.80[AFR][1000 genomes]
rs17489365	1.00[JPT][hapmap]
rs17489410	1.00[JPT][hapmap]
rs17489417	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489466	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs17489501	1.00[JPT][hapmap]
rs17489522	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489583	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489590	1.00[JPT][hapmap]
rs17489597	1.00[JPT][hapmap]
rs17489638	1.00[JPT][hapmap]
rs17489869	1.00[JPT][hapmap]
rs17490006	1.00[JPT][hapmap]
rs17490334	1.00[JPT][hapmap]
rs17490341	1.00[JPT][hapmap]
rs17490599	1.00[JPT][hapmap]
rs17518057	1.00[JPT][hapmap]
rs17518071	1.00[JPT][hapmap]
rs17518141	1.00[JPT][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518148	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518155	1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518190	1.00[AMR][1000 genomes]
rs17518204	1.00[JPT][hapmap]
rs17518232	1.00[JPT][hapmap]
rs17518322	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518329	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518343	1.00[JPT][hapmap]
rs17518357	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518392	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518413	1.00[JPT][hapmap]
rs17518420	1.00[JPT][hapmap]
rs17518427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518532	1.00[JPT][hapmap]
rs17518910	1.00[JPT][hapmap]
rs17519531	1.00[JPT][hapmap]
rs17519566	1.00[JPT][hapmap]
rs17519580	1.00[JPT][hapmap]
rs28365178	1.00[JPT][hapmap]
rs28365191	1.00[JPT][hapmap]
rs28365203	1.00[JPT][hapmap]
rs28365211	1.00[JPT][hapmap]
rs28365682	1.00[JPT][hapmap]
rs28365690	1.00[JPT][hapmap]
rs28370601	1.00[JPT][hapmap]
rs28370605	1.00[JPT][hapmap]
rs28370608	1.00[JPT][hapmap]
rs28370616	1.00[JPT][hapmap]
rs28370643	1.00[JPT][hapmap]
rs28370649	1.00[JPT][hapmap]
rs28370652	1.00[JPT][hapmap]
rs28370655	1.00[JPT][hapmap]
rs28370658	1.00[JPT][hapmap]
rs28370665	1.00[JPT][hapmap]
rs28370670	1.00[JPT][hapmap]
rs28370672	1.00[JPT][hapmap]
rs28370673	1.00[JPT][hapmap]
rs28370682	1.00[JPT][hapmap]
rs28370686	1.00[JPT][hapmap]
rs28370687	1.00[AMR][1000 genomes]
rs28370690	1.00[JPT][hapmap]
rs28370691	1.00[AMR][1000 genomes]
rs28370692	1.00[JPT][hapmap]
rs28370696	1.00[JPT][hapmap]
rs28370700	1.00[JPT][hapmap]
rs28370707	1.00[JPT][hapmap]
rs28370710	1.00[AMR][1000 genomes]
rs28370715	1.00[AMR][1000 genomes]
rs28370716	1.00[AMR][1000 genomes]
rs28370718	1.00[JPT][hapmap]
rs28370731	1.00[JPT][hapmap]
rs28370737	1.00[JPT][hapmap]
rs28370744	1.00[JPT][hapmap]
rs28370749	1.00[AMR][1000 genomes]
rs28370750	1.00[JPT][hapmap]
rs28370751	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370755	1.00[JPT][hapmap]
rs28370760	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370763	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370764	1.00[JPT][hapmap]
rs28370765	1.00[JPT][hapmap]
rs28370767	1.00[JPT][hapmap]
rs28370768	1.00[JPT][hapmap]
rs28370769	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370771	1.00[JPT][hapmap]
rs28370772	1.00[JPT][hapmap]
rs28370775	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370776	1.00[JPT][hapmap]
rs28370779	1.00[JPT][hapmap]
rs28370781	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370782	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370787	1.00[JPT][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370788	1.00[AMR][1000 genomes]
rs28370789	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370791	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370793	1.00[JPT][hapmap]
rs28370796	1.00[JPT][hapmap]
rs28370800	1.00[JPT][hapmap]
rs28370806	1.00[JPT][hapmap]
rs28370808	1.00[JPT][hapmap]
rs28370813	1.00[JPT][hapmap]
rs28370818	1.00[JPT][hapmap]
rs28370823	1.00[JPT][hapmap]
rs28370826	1.00[JPT][hapmap]
rs28740215	1.00[AMR][1000 genomes]
rs28740216	1.00[AMR][1000 genomes]
rs4405389	1.00[JPT][hapmap]
rs56193998	1.00[AMR][1000 genomes]
rs57966079	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs58812092	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59404097	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs59663144	1.00[AMR][1000 genomes]
rs60755503	1.00[AMR][1000 genomes]
rs61339615	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs74088130	1.00[AMR][1000 genomes]
rs74088192	1.00[AMR][1000 genomes]
rs74089321	1.00[AMR][1000 genomes]
rs74091033	1.00[AMR][1000 genomes]

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv558596	chr12:40413698-40591117	Active TSS Flanking Active TSS Bivalent Enhancer Enhancers Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:40394400-40448400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
2	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
3	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
4	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
6	chr12:40442200-40447600	Weak transcription	A549	lung
7	chr12:40442200-40451400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr12:40444000-40453400	Weak transcription	Right Ventricle	heart
9	chr12:40444400-40447600	Weak transcription	Colon Smooth Muscle	Colon
10	chr12:40445000-40448400	Weak transcription	Fetal Stomach	stomach
11	chr12:40445000-40448600	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr12:40445200-40445400	Enhancers	K562	blood

Quick Search:

Input of quick search could be:

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

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links