Variant report

Variant	rs12665850
Chromosome Location	chr6:144662744-144662745
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MYBL2	chr6:144662530-144663799	HepG2	liver:	n/a	n/a
2	FOXA2	chr6:144661363-144663185	HepG2	liver:	n/a	n/a
3	TCF7L2	chr6:144662159-144662806	Hela-S3	cervix:	n/a	chr6:144662598-144662607 chr6:144662594-144662610 chr6:144662595-144662609 chr6:144662594-144662610 chr6:144662347-144662356
4	FOXA1	chr6:144662629-144663141	HepG2	liver:	n/a	chr6:144662876-144662891

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:144658220..144661109-chr6:144661857..144663367,2	K562	blood:
2	chr6:144651662..144654238-chr6:144661982..144664850,2	MCF-7	breast:

Variant related genes	Relation type
UTRN	TF binding region

Extended variants
information (count: 130 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:126)

rs_ID	r²[population]
rs12660406	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12660513	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12660531	0.83[JPT][hapmap];1.00[EUR][1000 genomes]
rs12660596	1.00[EUR][1000 genomes]
rs12661781	1.00[EUR][1000 genomes]
rs12661969	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12662267	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12662696	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12662724	1.00[EUR][1000 genomes]
rs12662786	1.00[EUR][1000 genomes]
rs12662872	1.00[EUR][1000 genomes]
rs12662904	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12662914	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs12663172	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12663380	1.00[CHB][hapmap];1.00[JPT][hapmap];0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12663605	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12663851	1.00[EUR][1000 genomes]
rs12664200	1.00[EUR][1000 genomes]
rs12664245	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12664298	1.00[EUR][1000 genomes]
rs12664304	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12665589	1.00[EUR][1000 genomes]
rs17073442	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073463	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073482	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073498	1.00[EUR][1000 genomes]
rs17073506	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073509	1.00[AFR][1000 genomes]
rs17073524	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073528	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073529	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073539	1.00[AFR][1000 genomes]
rs17073544	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17073571	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073580	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073598	1.00[EUR][1000 genomes]
rs17073602	1.00[EUR][1000 genomes]
rs17073610	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073623	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073629	1.00[EUR][1000 genomes]
rs17073631	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17073672	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs17073678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17840301	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs1998367	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34140249	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34502493	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs34643516	1.00[AFR][1000 genomes]
rs35325795	1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35681372	1.00[EUR][1000 genomes]
rs36007040	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs3811097	1.00[EUR][1000 genomes]
rs4301321	1.00[EUR][1000 genomes]
rs4896714	1.00[EUR][1000 genomes]
rs4896715	1.00[EUR][1000 genomes]
rs4896717	1.00[EUR][1000 genomes]
rs55684976	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56820385	1.00[EUR][1000 genomes]
rs56897751	1.00[EUR][1000 genomes]
rs57069580	1.00[EUR][1000 genomes]
rs57380483	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57485302	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57592921	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57679521	1.00[EUR][1000 genomes]
rs57704478	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs57712072	1.00[EUR][1000 genomes]
rs57751197	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58084770	1.00[EUR][1000 genomes]
rs58396690	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58590469	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58646546	0.87[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs58847604	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58849686	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58857193	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs58981502	1.00[AFR][1000 genomes]
rs59003501	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59612420	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs59614628	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59718967	1.00[EUR][1000 genomes]
rs59803839	1.00[EUR][1000 genomes]
rs59810504	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs59892317	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs59936141	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60053855	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60188478	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60234245	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60345197	1.00[EUR][1000 genomes]
rs60439721	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60484357	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60559108	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60634096	1.00[EUR][1000 genomes]
rs60661533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60762289	1.00[EUR][1000 genomes]
rs60811448	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs60857439	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60859726	1.00[EUR][1000 genomes]
rs61087655	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61211447	1.00[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs61249035	1.00[EUR][1000 genomes]
rs61327932	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6914753	1.00[EUR][1000 genomes]
rs6915621	1.00[EUR][1000 genomes]
rs6917261	1.00[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6922109	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6922608	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6927798	1.00[EUR][1000 genomes]
rs73589002	1.00[EUR][1000 genomes]
rs73591113	1.00[EUR][1000 genomes]
rs73594934	1.00[EUR][1000 genomes]
rs73780508	1.00[EUR][1000 genomes]
rs73780540	1.00[EUR][1000 genomes]
rs7741466	1.00[EUR][1000 genomes]
rs7745240	1.00[EUR][1000 genomes]
rs7747486	1.00[EUR][1000 genomes]
rs7751351	1.00[EUR][1000 genomes]
rs7751876	1.00[EUR][1000 genomes]
rs7754883	1.00[EUR][1000 genomes]
rs7766883	1.00[EUR][1000 genomes]
rs7768531	1.00[EUR][1000 genomes]
rs7774175	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9484874	1.00[EUR][1000 genomes]
rs9496932	1.00[EUR][1000 genomes]
rs9496935	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9496938	1.00[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9496944	0.84[CHB][hapmap];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9496955	1.00[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	nsv830832	chr6:144572378-144759023	Weak transcription Active TSS Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	esv2422260	chr6:144574591-144731630	Weak transcription Flanking Active TSS ZNF genes & repeats Enhancers Active TSS Genic enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
3	nsv1031253	chr6:144599055-144883013	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases
4	nsv538461	chr6:144599055-144883013	Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	11 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:109 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:144643800-144663000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:144648800-144672800	Weak transcription	Fetal Stomach	stomach
3	chr6:144652000-144668200	Weak transcription	Aorta	Aorta
4	chr6:144653200-144684600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr6:144653400-144662800	Weak transcription	Osteobl	bone
6	chr6:144653400-144665200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr6:144653600-144665000	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr6:144656000-144664200	Weak transcription	Fetal Kidney	kidney
9	chr6:144656000-144665200	Weak transcription	H1 Cell Line	embryonic stem cell
10	chr6:144656000-144665200	Weak transcription	HUES6 Cell Line	embryonic stem cell
11	chr6:144656000-144668400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr6:144656000-144670600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
13	chr6:144656600-144664800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr6:144657000-144670800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr6:144657200-144664000	Enhancers	Primary B cells from cord blood	blood
16	chr6:144657200-144664800	Enhancers	Primary B cells from peripheral blood	blood
17	chr6:144657200-144665200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr6:144657400-144665000	Weak transcription	Muscle Satellite Cultured Cells	--
19	chr6:144657600-144662800	Weak transcription	Brain Substantia Nigra	brain
20	chr6:144657800-144666400	Weak transcription	Fetal Muscle Trunk	muscle
21	chr6:144658200-144664400	Weak transcription	Fetal Intestine Large	intestine
22	chr6:144658200-144668200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr6:144658400-144662800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr6:144658400-144664000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:144658400-144664400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
26	chr6:144658400-144670400	Weak transcription	Fetal Lung	lung
27	chr6:144658600-144662800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr6:144658600-144664000	Weak transcription	Fetal Intestine Small	intestine
29	chr6:144658600-144664000	Weak transcription	Fetal Thymus	thymus
30	chr6:144659000-144663000	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr6:144659200-144664800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
32	chr6:144659600-144665200	Enhancers	Primary monocytes fromperipheralblood	blood
33	chr6:144659800-144662800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
34	chr6:144659800-144664800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:144660000-144663000	Weak transcription	Psoas Muscle	Psoas
36	chr6:144660000-144663600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr6:144660000-144665400	Enhancers	Primary hematopoietic stem cells	blood
38	chr6:144660000-144667800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr6:144660200-144664600	Enhancers	Primary hematopoietic stem cells short term culture	blood
40	chr6:144660200-144665000	Enhancers	NHEK	skin
41	chr6:144660200-144665200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr6:144660200-144667600	Weak transcription	Placenta	Placenta
43	chr6:144660400-144662800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr6:144660400-144663400	Enhancers	Breast Myoepithelial Primary Cells	Breast
45	chr6:144660400-144664000	Weak transcription	Thymus	Thymus
46	chr6:144660400-144668200	Weak transcription	Brain Hippocampus Middle	brain
47	chr6:144660400-144670800	Weak transcription	Colon Smooth Muscle	Colon
48	chr6:144660800-144665400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
49	chr6:144661000-144663400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr6:144661000-144663600	Enhancers	Hela-S3	cervix

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