Variant report

Variant	rs17489225
Chromosome Location	chr12:40438905-40438906
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	chr12:40434942..40437888-chr12:40438406..40442021,3	MCF-7	breast:
2	12:40436818-40441273..12:40703633-40711447	GM12878	blood:

Variant related genes	Relation type
ENSG00000188906	Chromatin interaction

Extended variants
information (count: 149 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:145)

rs_ID	r²[population]
rs12368785	1.00[JPT][hapmap]
rs12368891	1.00[JPT][hapmap]
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]
rs17458182	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]
rs17489218	1.00[JPT][hapmap]
rs17489246	1.00[JPT][hapmap]
rs17489253	1.00[JPT][hapmap]
rs17489267	1.00[JPT][hapmap]
rs17489302	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489365	1.00[JPT][hapmap]
rs17489379	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489410	1.00[JPT][hapmap]
rs17489417	1.00[JPT][hapmap]
rs17489466	1.00[JPT][hapmap]
rs17489501	1.00[JPT][hapmap]
rs17489583	1.00[JPT][hapmap]
rs17489590	1.00[JPT][hapmap]
rs17489597	1.00[JPT][hapmap]
rs17489638	1.00[JPT][hapmap]
rs17489666	1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489715	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489722	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17489869	1.00[JPT][hapmap]
rs17489889	1.00[AMR][1000 genomes]
rs17490006	1.00[JPT][hapmap]
rs17490334	1.00[JPT][hapmap]
rs17490341	1.00[JPT][hapmap]
rs17490418	1.00[AMR][1000 genomes]
rs17490578	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17490585	1.00[AMR][1000 genomes]
rs17490599	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17490620	1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17518014	1.00[AMR][1000 genomes]
rs17518050	1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518057	1.00[JPT][hapmap]
rs17518071	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518141	1.00[JPT][hapmap]
rs17518148	1.00[JPT][hapmap]
rs17518155	1.00[JPT][hapmap]
rs17518204	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518232	1.00[JPT][hapmap]
rs17518253	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518273	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518343	1.00[JPT][hapmap]
rs17518364	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs17518413	1.00[JPT][hapmap]
rs17518420	1.00[JPT][hapmap]
rs17518532	1.00[JPT][hapmap]
rs17518770	1.00[AMR][1000 genomes]
rs17518805	1.00[AMR][1000 genomes]
rs17518910	1.00[JPT][hapmap]
rs17518992	1.00[AMR][1000 genomes]
rs17519531	1.00[JPT][hapmap]
rs17519566	1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes]
rs17519580	1.00[JPT][hapmap]
rs2708450	1.00[AMR][1000 genomes]
rs2708451	1.00[AMR][1000 genomes]
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]
rs28370688	1.00[AMR][1000 genomes]
rs28370690	1.00[JPT][hapmap]
rs28370692	1.00[JPT][hapmap]
rs28370696	1.00[JPT][hapmap]
rs28370700	1.00[JPT][hapmap]
rs28370707	1.00[JPT][hapmap]
rs28370717	1.00[JPT][hapmap]
rs28370718	1.00[JPT][hapmap]
rs28370731	1.00[JPT][hapmap]
rs28370737	1.00[JPT][hapmap]
rs28370744	1.00[JPT][hapmap]
rs28370745	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370748	1.00[AMR][1000 genomes]
rs28370750	1.00[JPT][hapmap]
rs28370751	1.00[JPT][hapmap]
rs28370755	1.00[JPT][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370758	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];1.00[AMR][1000 genomes]
rs28370771	1.00[JPT][hapmap]
rs28370772	1.00[JPT][hapmap]
rs28370776	1.00[JPT][hapmap];1.00[AMR][1000 genomes]
rs28370777	1.00[AMR][1000 genomes]
rs28370778	1.00[AMR][1000 genomes]
rs28370779	1.00[JPT][hapmap]
rs28370780	1.00[AMR][1000 genomes]
rs28370783	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs28370786	1.00[AMR][1000 genomes]
rs28370787	1.00[JPT][hapmap]
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]
rs28740189	1.00[JPT][hapmap]
rs4405389	1.00[JPT][hapmap]
rs7306747	1.00[AMR][1000 genomes]
rs7307258	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046428	chr12:40226283-40439843	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
2	nsv541481	chr12:40226283-40439843	Enhancers Flanking Active TSS Weak transcription ZNF genes & repeats Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region miRNA target site	6 gene(s)	inside rSNPs	diseases
3	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
4	nsv558597	chr12:40414631-40442892	Weak transcription Enhancers Active TSS Flanking Active TSS Strong transcription ZNF genes & repeats	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:11 , 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	chr12:40405400-40445200	Weak transcription	K562	blood
3	chr12:40416600-40441800	Weak transcription	Ovary	ovary
4	chr12:40419000-40447600	Weak transcription	Hela-S3	cervix
5	chr12:40421600-40453400	Weak transcription	Left Ventricle	heart
6	chr12:40426400-40452800	Weak transcription	Sigmoid Colon	Sigmoid Colon
7	chr12:40428000-40452600	Weak transcription	Fetal Intestine Small	intestine
8	chr12:40429400-40441000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
9	chr12:40434000-40441600	Weak transcription	Pancreatic Islets	Pancreatic Islet
10	chr12:40438400-40440200	Enhancers	Fetal Brain Male	brain
11	chr12:40438800-40439600	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived

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