Variant report

Variant	rs10040840
Chromosome Location	chr5:126224390-126224391
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr5:126217612..126219765-chr5:126223555..126225537,2	MCF-7	breast:

Extended variants
information (count: 192 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:188)

rs_ID	r²[population]
rs10519919	0.82[EUR][1000 genomes]
rs10519922	0.82[EUR][1000 genomes]
rs10519923	0.82[EUR][1000 genomes]
rs12518420	0.82[EUR][1000 genomes]
rs12651864	0.82[EUR][1000 genomes]
rs12652390	0.81[CHD][hapmap];0.81[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12652417	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653000	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12653290	0.82[EUR][1000 genomes]
rs12653444	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12653823	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12654717	1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12654725	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12654808	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12655006	1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12655199	0.82[EUR][1000 genomes]
rs12655223	0.82[GIH][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12655258	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12655319	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12655435	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12655605	0.82[EUR][1000 genomes]
rs12655699	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12655726	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs12655928	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs12655991	0.80[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12656236	0.82[EUR][1000 genomes]
rs12656537	0.82[JPT][hapmap];0.82[EUR][1000 genomes]
rs12656837	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12658138	0.82[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12658174	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12658599	0.85[JPT][hapmap];0.82[EUR][1000 genomes]
rs12658816	0.82[EUR][1000 genomes]
rs12658821	0.82[EUR][1000 genomes]
rs12658822	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs12659476	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12659607	0.82[EUR][1000 genomes]
rs12659614	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs12659633	0.82[EUR][1000 genomes]
rs17165192	0.82[EUR][1000 genomes]
rs17165194	0.82[EUR][1000 genomes]
rs17165211	0.82[EUR][1000 genomes]
rs17165213	0.89[GIH][hapmap];1.00[TSI][hapmap]
rs17165228	0.81[CHD][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17165234	1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17165239	0.82[EUR][1000 genomes]
rs17165244	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs17165248	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs17165249	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs17165251	1.00[CHB][hapmap];0.96[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap]
rs34416835	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs34738240	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35566904	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs35627668	0.82[EUR][1000 genomes]
rs36091921	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3812061	0.81[CHD][hapmap];0.82[GIH][hapmap];0.85[JPT][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs4141169	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs4141170	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap]
rs55792418	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55802546	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56094173	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56122855	0.89[ASN][1000 genomes]
rs56124224	0.82[EUR][1000 genomes]
rs56272610	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs56688052	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs56689722	0.82[EUR][1000 genomes]
rs56786115	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57031083	1.00[EUR][1000 genomes]
rs57032367	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57052202	0.82[EUR][1000 genomes]
rs57081850	0.82[EUR][1000 genomes]
rs57113926	1.00[EUR][1000 genomes]
rs57485054	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57627287	0.82[EUR][1000 genomes]
rs57700815	0.82[EUR][1000 genomes]
rs57833976	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57915728	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58164143	0.82[EUR][1000 genomes]
rs58249730	0.93[ASN][1000 genomes]
rs58262537	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58527455	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs58646561	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs58838495	1.00[EUR][1000 genomes]
rs58894799	0.82[EUR][1000 genomes]
rs59459356	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59489123	0.82[EUR][1000 genomes]
rs59643871	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59676931	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs59814275	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60045571	1.00[EUR][1000 genomes]
rs60138815	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60615137	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60636815	0.82[EUR][1000 genomes]
rs60781824	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs60889784	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61031864	0.82[EUR][1000 genomes]
rs61258380	0.82[EUR][1000 genomes]
rs61279308	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs61463824	1.00[EUR][1000 genomes]
rs61496590	1.00[EUR][1000 genomes]
rs61647801	0.82[EUR][1000 genomes]
rs61653213	0.82[EUR][1000 genomes]
rs61685918	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6595747	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs6860581	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap]
rs6862462	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6864607	1.00[CHB][hapmap];1.00[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6870711	0.86[GIH][hapmap]
rs6872893	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6877692	1.00[CHB][hapmap];0.96[CHD][hapmap];0.96[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs6882025	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[EUR][1000 genomes]
rs6883181	0.82[EUR][1000 genomes]
rs6886131	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs6888532	0.82[EUR][1000 genomes]
rs6893763	0.82[EUR][1000 genomes]
rs6899030	0.82[EUR][1000 genomes]
rs72505648	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335426	1.00[EUR][1000 genomes]
rs73335444	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335447	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335461	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335474	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73335490	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73335494	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73335498	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73335501	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73337225	0.89[ASN][1000 genomes]
rs73337229	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73337233	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73337299	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73783476	0.96[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73783496	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73783501	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73783503	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73783504	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73783506	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73783507	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786207	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786209	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786212	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786239	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786240	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786241	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786242	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786244	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786246	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786247	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786249	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786250	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786251	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786252	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786253	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786255	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786259	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786260	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786261	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786262	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786264	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786265	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786266	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786267	0.93[ASN][1000 genomes]
rs73786268	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786269	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786270	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786271	0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73786272	0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73786276	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786277	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786278	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786280	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786281	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786282	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786283	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786284	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786285	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786287	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786288	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786290	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786294	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786295	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73786298	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73787403	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73787404	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs73787406	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7701976	0.94[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7709865	1.00[CHB][hapmap];0.96[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs7715377	1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7727719	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9918233	1.00[CHB][hapmap];0.86[JPT][hapmap];0.82[EUR][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	nsv949054	chr5:125918148-126254480	Enhancers Genic enhancers Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
2	nsv534292	chr5:125993451-126259315	Flanking Active TSS Active TSS Enhancers Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
3	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
4	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

No data

Chromatin state (count:25 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:126201800-126253400	Weak transcription	A549	lung
2	chr5:126205200-126245600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr5:126205400-126245600	Weak transcription	Primary hematopoietic stem cells	blood
4	chr5:126205600-126238200	Weak transcription	Primary T cells from cord blood	blood
5	chr5:126211200-126231600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr5:126212000-126236800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr5:126214200-126237400	Weak transcription	Fetal Brain Female	brain
8	chr5:126214200-126238600	Weak transcription	Fetal Muscle Leg	muscle
9	chr5:126214200-126238600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr5:126214200-126245400	Weak transcription	Fetal Muscle Trunk	muscle
11	chr5:126214600-126232000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr5:126214600-126245200	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr5:126214600-126250400	Weak transcription	Pancreas	Pancrea
14	chr5:126214800-126255200	Weak transcription	Psoas Muscle	Psoas
15	chr5:126215400-126245000	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr5:126220400-126225400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
17	chr5:126220400-126238400	Weak transcription	Ovary	ovary
18	chr5:126220600-126236000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr5:126220600-126238400	Weak transcription	Left Ventricle	heart
20	chr5:126220800-126237000	Weak transcription	HSMM	muscle
21	chr5:126220800-126237600	Weak transcription	Right Ventricle	heart
22	chr5:126220800-126245400	Weak transcription	HUVEC	blood vessel
23	chr5:126223200-126224400	Strong transcription	Primary B cells from cord blood	blood
24	chr5:126224000-126232000	Weak transcription	H9 Cell Line	embryonic stem cell
25	chr5:126224000-126238400	Weak transcription	K562	blood

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