Variant report

Variant	rs12659614
Chromosome Location	chr5:126371307-126371308
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr5:126364056..126368822-chr5:126369920..126375542,6	MCF-7	breast:
2	chr5:126365480..126368335-chr5:126368822..126372507,5	MCF-7	breast:
3	chr5:126181775..126183467-chr5:126371071..126372584,2	K562	blood:
4	chr5:126370055..126372210-chr5:126405124..126407966,2	K562	blood:
5	chr5:126368719..126372377-chr5:126376805..126380284,3	K562	blood:
6	chr5:126370445..126372377-chr5:126376805..126378615,2	K562	blood:

Variant related genes	Relation type
ENSG00000173926	Chromatin interaction
ENSG00000164241	Chromatin interaction

Extended variants
information (count: 196 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:194)

rs_ID	r²[population]
rs10040840	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs10519919	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10519922	1.00[EUR][1000 genomes]
rs10519923	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12518420	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12651864	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12652019	0.91[EUR][1000 genomes]
rs12652390	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12652417	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12653000	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12653290	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12653444	1.00[EUR][1000 genomes]
rs12654313	0.91[EUR][1000 genomes]
rs12654717	1.00[EUR][1000 genomes]
rs12654725	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12654808	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12655006	0.84[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12655199	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655223	1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.85[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12655258	0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12655319	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12655435	1.00[EUR][1000 genomes]
rs12655605	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12655699	0.85[JPT][hapmap]
rs12655726	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs12655928	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12655991	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12656236	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12656537	0.85[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12656837	0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12658138	0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12658174	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12658599	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658608	0.83[AFR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658816	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12658821	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12658822	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12659476	0.82[JPT][hapmap];1.00[EUR][1000 genomes]
rs12659607	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12659633	1.00[EUR][1000 genomes]
rs17165192	1.00[EUR][1000 genomes]
rs17165194	1.00[EUR][1000 genomes]
rs17165211	1.00[EUR][1000 genomes]
rs17165213	1.00[TSI][hapmap]
rs17165228	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17165234	0.84[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17165239	1.00[EUR][1000 genomes]
rs17165244	0.85[JPT][hapmap]
rs17165248	0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs17165249	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs17165251	0.87[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap]
rs17762544	0.91[EUR][1000 genomes]
rs17839703	0.92[EUR][1000 genomes]
rs34416835	1.00[EUR][1000 genomes]
rs34738240	1.00[EUR][1000 genomes]
rs35566904	1.00[EUR][1000 genomes]
rs35627668	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36091921	1.00[EUR][1000 genomes]
rs3812061	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs4141169	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs4141170	0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs55792418	1.00[EUR][1000 genomes]
rs55802546	1.00[EUR][1000 genomes]
rs56094173	1.00[EUR][1000 genomes]
rs56122855	0.92[EUR][1000 genomes]
rs56124224	1.00[EUR][1000 genomes]
rs56171951	0.92[EUR][1000 genomes]
rs56272610	1.00[EUR][1000 genomes]
rs56688052	1.00[EUR][1000 genomes]
rs56689722	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56786115	1.00[EUR][1000 genomes]
rs57031083	1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57032367	1.00[EUR][1000 genomes]
rs57052202	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57081850	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57113926	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs57485054	0.82[EUR][1000 genomes]
rs57627287	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57700815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57833976	1.00[EUR][1000 genomes]
rs57906418	0.92[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs57915728	1.00[EUR][1000 genomes]
rs58164143	1.00[EUR][1000 genomes]
rs58249730	0.91[EUR][1000 genomes]
rs58262537	1.00[EUR][1000 genomes]
rs58527455	1.00[EUR][1000 genomes]
rs58646561	1.00[EUR][1000 genomes]
rs58838495	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs58894799	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59459356	1.00[EUR][1000 genomes]
rs59489123	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs59643871	1.00[EUR][1000 genomes]
rs59676931	1.00[EUR][1000 genomes]
rs59814275	1.00[EUR][1000 genomes]
rs60045571	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs60138815	1.00[EUR][1000 genomes]
rs60244211	0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60615137	1.00[EUR][1000 genomes]
rs60636815	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60781824	1.00[EUR][1000 genomes]
rs60889784	1.00[EUR][1000 genomes]
rs61031864	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61258380	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61279308	1.00[EUR][1000 genomes]
rs61463824	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61496590	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs61647801	0.80[ASN][1000 genomes]
rs61653213	0.83[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61685918	1.00[EUR][1000 genomes]
rs6595747	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs6860581	0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs6862462	1.00[EUR][1000 genomes]
rs6864607	0.81[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6872893	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs6877692	0.84[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs6882025	0.85[JPT][hapmap];1.00[EUR][1000 genomes]
rs6883181	1.00[EUR][1000 genomes]
rs6886131	0.85[JPT][hapmap]
rs6888532	1.00[EUR][1000 genomes]
rs6893763	1.00[EUR][1000 genomes]
rs6899030	1.00[EUR][1000 genomes]
rs72505648	0.82[EUR][1000 genomes]
rs73335426	0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs73335444	0.82[EUR][1000 genomes]
rs73335447	0.82[EUR][1000 genomes]
rs73335461	0.82[EUR][1000 genomes]
rs73335474	0.82[EUR][1000 genomes]
rs73335490	1.00[EUR][1000 genomes]
rs73335494	1.00[EUR][1000 genomes]
rs73335498	1.00[EUR][1000 genomes]
rs73335501	1.00[EUR][1000 genomes]
rs73337225	0.84[EUR][1000 genomes]
rs73337229	1.00[EUR][1000 genomes]
rs73337233	1.00[EUR][1000 genomes]
rs73337299	1.00[EUR][1000 genomes]
rs73783476	0.82[EUR][1000 genomes]
rs73783496	1.00[EUR][1000 genomes]
rs73783501	1.00[EUR][1000 genomes]
rs73783503	1.00[EUR][1000 genomes]
rs73783504	1.00[EUR][1000 genomes]
rs73783506	1.00[EUR][1000 genomes]
rs73783507	1.00[EUR][1000 genomes]
rs73786207	1.00[EUR][1000 genomes]
rs73786209	1.00[EUR][1000 genomes]
rs73786212	1.00[EUR][1000 genomes]
rs73786239	1.00[EUR][1000 genomes]
rs73786240	1.00[EUR][1000 genomes]
rs73786241	1.00[EUR][1000 genomes]
rs73786242	1.00[EUR][1000 genomes]
rs73786244	1.00[EUR][1000 genomes]
rs73786246	1.00[EUR][1000 genomes]
rs73786247	1.00[EUR][1000 genomes]
rs73786249	1.00[EUR][1000 genomes]
rs73786250	1.00[EUR][1000 genomes]
rs73786251	1.00[EUR][1000 genomes]
rs73786252	1.00[EUR][1000 genomes]
rs73786253	1.00[EUR][1000 genomes]
rs73786255	1.00[EUR][1000 genomes]
rs73786259	1.00[EUR][1000 genomes]
rs73786260	1.00[EUR][1000 genomes]
rs73786261	1.00[EUR][1000 genomes]
rs73786262	1.00[EUR][1000 genomes]
rs73786264	1.00[EUR][1000 genomes]
rs73786265	1.00[EUR][1000 genomes]
rs73786266	1.00[EUR][1000 genomes]
rs73786267	0.92[EUR][1000 genomes]
rs73786268	1.00[EUR][1000 genomes]
rs73786269	1.00[EUR][1000 genomes]
rs73786270	1.00[EUR][1000 genomes]
rs73786271	1.00[EUR][1000 genomes]
rs73786272	1.00[EUR][1000 genomes]
rs73786276	1.00[EUR][1000 genomes]
rs73786277	1.00[EUR][1000 genomes]
rs73786278	1.00[EUR][1000 genomes]
rs73786280	1.00[EUR][1000 genomes]
rs73786281	1.00[EUR][1000 genomes]
rs73786282	1.00[EUR][1000 genomes]
rs73786283	1.00[EUR][1000 genomes]
rs73786284	1.00[EUR][1000 genomes]
rs73786285	1.00[EUR][1000 genomes]
rs73786287	1.00[EUR][1000 genomes]
rs73786288	1.00[EUR][1000 genomes]
rs73786290	1.00[EUR][1000 genomes]
rs73786294	1.00[EUR][1000 genomes]
rs73786295	1.00[EUR][1000 genomes]
rs73786298	1.00[EUR][1000 genomes]
rs73787403	1.00[EUR][1000 genomes]
rs73787404	1.00[EUR][1000 genomes]
rs73787406	1.00[EUR][1000 genomes]
rs7701976	0.81[CHD][hapmap];0.96[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs7709865	0.84[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap]
rs7715377	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs7727719	0.82[EUR][1000 genomes]
rs9918233	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1024265	chr5:126213004-126691163	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv869897	chr5:126224358-126445210	Weak transcription Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12659614	PTH2	trans	lymphoblastoid	seeQTL

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126367600-126375800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr5:126367600-126376000	Weak transcription	Left Ventricle	heart
3	chr5:126367600-126376600	Weak transcription	Right Atrium	heart
4	chr5:126367600-126382000	Weak transcription	Primary B cells from cord blood	blood
5	chr5:126367600-126391800	Weak transcription	GM12878-XiMat	blood
6	chr5:126367800-126373200	Weak transcription	Fetal Heart	heart
7	chr5:126367800-126376600	Weak transcription	Pancreas	Pancrea
8	chr5:126368000-126376400	Weak transcription	K562	blood
9	chr5:126368000-126387200	Weak transcription	Primary T helper cells PMA-I stimulated	--
10	chr5:126370200-126379000	Weak transcription	Primary T cells from cord blood	blood

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