Variant report

Variant	rs129310
Chromosome Location	chr3:50594836-50594837
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:50483163..50485721-chr3:50593817..50596620,2	MCF-7	breast:
2	chr3:50594685..50598509-chr3:50599030..50605276,6	K562	blood:
3	chr3:50593486..50596662-chr3:50604941..50607206,3	MCF-7	breast:
4	chr3:50593179..50595376-chr3:50596948..50598840,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000114735	Chromatin interaction
ENSG00000088543	Chromatin interaction

Extended variants
information (count: 105 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:91)

rs_ID	r²[population]
rs1013233	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs1034405	1.00[CEU][hapmap];0.83[YRI][hapmap];0.90[EUR][1000 genomes]
rs11130252	0.85[EUR][1000 genomes]
rs11712367	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs11716398	0.85[AMR][1000 genomes]
rs11719998	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12491425	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12493985	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12639126	0.81[CEU][hapmap]
rs13076850	0.88[EUR][1000 genomes]
rs13083004	0.90[EUR][1000 genomes]
rs13084476	0.83[EUR][1000 genomes]
rs13091933	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs13094336	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1385025	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs175634	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17787569	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs1824281	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs1971976	0.84[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs201193	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs201194	0.94[CEU][hapmap];0.88[EUR][1000 genomes]
rs201196	0.90[EUR][1000 genomes]
rs201198	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2227280	0.89[EUR][1000 genomes]
rs2232248	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2232253	0.89[EUR][1000 genomes]
rs2269505	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2269507	0.89[EUR][1000 genomes]
rs2355321	0.89[EUR][1000 genomes]
rs2355323	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34202063	0.89[EUR][1000 genomes]
rs34399912	0.89[EUR][1000 genomes]
rs34584636	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs34756253	0.83[EUR][1000 genomes]
rs34848480	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs34889917	0.89[EUR][1000 genomes]
rs35655236	0.90[EUR][1000 genomes]
rs35690191	0.90[EUR][1000 genomes]
rs35714264	0.84[EUR][1000 genomes]
rs375544	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs3792325	0.91[CHB][hapmap];0.91[JPT][hapmap];0.87[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3792328	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs3804627	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3804632	0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs388483	0.85[YRI][hapmap]
rs391620	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3943212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.84[AFR][1000 genomes];0.85[AMR][1000 genomes]
rs396302	0.95[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs398703	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs399484	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs399971	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs414171	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs417592	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs441516	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs443030	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs443436	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs448028	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs4485709	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs453570	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4688712	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs490634	0.94[CEU][hapmap];0.86[EUR][1000 genomes]
rs59949730	0.89[EUR][1000 genomes]
rs616589	0.91[CHB][hapmap];0.82[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.86[AMR][1000 genomes]
rs628081	0.94[CEU][hapmap];0.87[JPT][hapmap];0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs6446212	1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[YRI][hapmap];0.84[AFR][1000 genomes]
rs6446213	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs67588094	0.89[EUR][1000 genomes]
rs6778680	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap]
rs6779819	1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[AMR][1000 genomes]
rs67813889	0.91[EUR][1000 genomes]
rs6784166	0.84[EUR][1000 genomes]
rs6787521	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs6796769	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs695170	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs71326937	0.89[EUR][1000 genomes]
rs728901	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs750453	0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs750510	0.88[CEU][hapmap];0.82[JPT][hapmap];0.80[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs751851	0.85[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs754298	0.81[EUR][1000 genomes]
rs7615703	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs7635666	0.85[AMR][1000 genomes]
rs7646236	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs808149	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs809454	0.86[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs813243	1.00[CHB][hapmap];0.95[JPT][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs900735	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes]
rs9682401	1.00[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs9825535	0.95[CHB][hapmap];0.95[JPT][hapmap]
rs9826757	1.00[CHB][hapmap];0.95[JPT][hapmap]
rs9830920	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:14 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1821728	chr3:50156142-50657253	Strong transcription Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Enhancers Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases
2	nsv876770	chr3:50158774-50609624	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
3	nsv1001993	chr3:50187646-50640808	Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	104 gene(s)	inside rSNPs	diseases
4	esv3584502	chr3:50368278-50659741	Strong transcription Bivalent/Poised TSS Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv432419	chr3:50388396-50637496	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases
6	nsv1013225	chr3:50440826-50700448	Flanking Active TSS Enhancers Genic enhancers Weak transcription Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
7	nsv536566	chr3:50440826-50700448	Genic enhancers Weak transcription Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
8	nsv984540	chr3:50473691-50669310	Enhancers Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
9	nsv1012501	chr3:50483037-50679591	Bivalent Enhancer Flanking Active TSS Enhancers Weak transcription Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
10	nsv536567	chr3:50483037-50679591	Bivalent Enhancer Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
11	nsv460532	chr3:50536273-50616049	Bivalent Enhancer Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
12	nsv590272	chr3:50536273-50616049	Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA target site	17 gene(s)	inside rSNPs	diseases
13	nsv460533	chr3:50574213-50678151	Bivalent/Poised TSS Weak transcription Enhancers Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
14	nsv590273	chr3:50574213-50678151	Weak transcription Active TSS Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:50578600-50595800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr3:50583600-50603400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
3	chr3:50586000-50597200	Weak transcription	Right Atrium	heart
4	chr3:50587600-50603800	Weak transcription	Brain Anterior Caudate	brain
5	chr3:50588400-50603600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:50589600-50604000	Weak transcription	Fetal Lung	lung
7	chr3:50589800-50595600	Weak transcription	Fetal Stomach	stomach
8	chr3:50592200-50596400	Enhancers	Fetal Muscle Leg	muscle
9	chr3:50592600-50597200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:50592800-50604000	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr3:50593200-50596000	Weak transcription	Ovary	ovary
12	chr3:50593200-50597000	Weak transcription	Skeletal Muscle Male	skeletal muscle
13	chr3:50593400-50601400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr3:50593400-50602800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr3:50593600-50604000	Weak transcription	Brain Cingulate Gyrus	brain
16	chr3:50593800-50596000	Weak transcription	Stomach Smooth Muscle	stomach
17	chr3:50593800-50604200	Weak transcription	Brain Germinal Matrix	brain
18	chr3:50594000-50595400	Bivalent Enhancer	HepG2	liver
19	chr3:50594000-50595800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
20	chr3:50594200-50595400	Bivalent Enhancer	Fetal Muscle Trunk	muscle
21	chr3:50594200-50596000	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr3:50594200-50596400	Enhancers	Fetal Heart	heart
23	chr3:50594200-50596400	Weak transcription	Skeletal Muscle Female	skeletal muscle
24	chr3:50594200-50604000	Weak transcription	Pancreas	Pancrea
25	chr3:50594400-50595000	Enhancers	Fetal Adrenal Gland	Adrenal Gland
26	chr3:50594400-50595800	Enhancers	Right Ventricle	heart
27	chr3:50594600-50596200	Weak transcription	Brain Angular Gyrus	brain
28	chr3:50594600-50597400	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr3:50594600-50604000	Weak transcription	Brain Substantia Nigra	brain
30	chr3:50594800-50601000	Weak transcription	Fetal Brain Female	brain
31	chr3:50594800-50604000	Weak transcription	Adipose Nuclei	Adipose

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