Variant report

Variant	rs225623
Chromosome Location	chr6:142467574-142467575
allele	A/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	CTCF	chr6:142467512-142468707	SK-N-SH	brain:	n/a	chr6:142468177-142468195
2	STAT3	chr6:142467413-142467808	MCF10A-Er-Src	breast:	n/a	n/a
3	JUN	chr6:142466776-142469076	K562	blood:	n/a	chr6:142468405-142468413 chr6:142467085-142467093 chr6:142468621-142468630 chr6:142467272-142467284
4	CTCF	chr6:142467474-142468624	A549	lung:	n/a	chr6:142468177-142468195

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:142460806..142463212-chr6:142465589..142468326,2	K562	blood:

Variant related genes	Relation type
VTA1	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:77)

rs_ID	r²[population]
rs11758623	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs178783	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225601	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225602	0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225604	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs225605	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap]
rs225606	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225618	0.84[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225620	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs225622	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225624	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225628	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225629	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs225630	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225631	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225632	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225633	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225634	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225635	0.81[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225636	0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225637	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs225639	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225640	0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225641	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225642	0.93[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225643	0.90[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs225650	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225651	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225652	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225653	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225654	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225655	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225656	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225657	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs225658	0.88[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225659	0.85[CEU][hapmap];0.84[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs225660	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225661	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs225662	0.86[CEU][hapmap];0.85[CHB][hapmap];1.00[JPT][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225663	0.84[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225664	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225665	0.85[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs225666	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225667	0.81[ASN][1000 genomes]
rs225668	0.81[ASN][1000 genomes]
rs225670	0.81[ASN][1000 genomes]
rs225671	0.83[CHB][hapmap];1.00[JPT][hapmap];0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs225672	0.81[ASN][1000 genomes]
rs225673	0.85[CHB][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs225674	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225675	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225676	0.83[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225677	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs225678	0.81[CHB][hapmap];1.00[JPT][hapmap]
rs225679	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225684	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs225685	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225687	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225688	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs225689	1.00[JPT][hapmap]
rs225695	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225700	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225701	1.00[JPT][hapmap]
rs225702	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs225710	0.83[CHB][hapmap];1.00[JPT][hapmap]
rs4896574	0.86[CEU][hapmap];0.91[JPT][hapmap]
rs4896575	0.89[CEU][hapmap];0.91[JPT][hapmap]
rs56185739	0.81[ASN][1000 genomes]
rs62430473	0.82[ASN][1000 genomes]
rs628311	0.93[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs639658	0.92[CEU][hapmap];0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs6939944	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6939975	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7776318	0.81[JPT][hapmap]
rs9321861	0.81[JPT][hapmap]
rs9389979	0.82[JPT][hapmap]
rs9389980	0.83[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886732	chr6:142290338-142536049	Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv886733	chr6:142316672-142514226	Weak transcription Enhancers Active TSS Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats 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	20 gene(s)	inside rSNPs	diseases
3	nsv886734	chr6:142347611-142523865	Weak transcription Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
4	nsv830824	chr6:142361107-142544929	Genic enhancers Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv886735	chr6:142365171-142472294	Enhancers Active TSS Weak transcription Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
6	nsv886736	chr6:142365171-142523865	Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Active TSS Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:45 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:142466400-142467600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
2	chr6:142466800-142467600	Enhancers	Brain Germinal Matrix	brain
3	chr6:142467000-142467800	Enhancers	Primary T helper cells PMA-I stimulated	--
4	chr6:142467200-142467600	Enhancers	Primary T helper naive cells from peripheral blood	blood
5	chr6:142467200-142467600	Active TSS	Liver	Liver
6	chr6:142467200-142467600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
7	chr6:142467200-142467600	Enhancers	Fetal Muscle Leg	muscle
8	chr6:142467200-142467600	Enhancers	Ovary	ovary
9	chr6:142467200-142467600	Enhancers	Rectal Smooth Muscle	rectum
10	chr6:142467200-142467600	Enhancers	Thymus	Thymus
11	chr6:142467200-142467600	Enhancers	A549	lung
12	chr6:142467200-142467800	Enhancers	Primary B cells from peripheral blood	blood
13	chr6:142467200-142467800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr6:142467200-142467800	Enhancers	Osteobl	bone
15	chr6:142467200-142468200	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr6:142467200-142469000	Active TSS	Brain Anterior Caudate	brain
17	chr6:142467200-142469000	Active TSS	Fetal Heart	heart
18	chr6:142467200-142469200	Active TSS	Skeletal Muscle Female	skeletal muscle
19	chr6:142467400-142467600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
20	chr6:142467400-142467600	Enhancers	Primary T cells from cord blood	blood
21	chr6:142467400-142467600	Enhancers	Primary hematopoietic stem cells short term culture	blood
22	chr6:142467400-142467600	Enhancers	Primary T helper cells fromperipheralblood	blood
23	chr6:142467400-142467600	Enhancers	Cortex derived primary cultured neurospheres	brain
24	chr6:142467400-142467600	Enhancers	Adipose Nuclei	Adipose
25	chr6:142467400-142467600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
26	chr6:142467400-142467600	Flanking Active TSS	HepG2	liver
27	chr6:142467400-142467600	Enhancers	NHEK	skin
28	chr6:142467400-142467800	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr6:142467400-142467800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
30	chr6:142467400-142467800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
31	chr6:142467400-142467800	Enhancers	Primary T killer memory cells from peripheral blood	blood
32	chr6:142467400-142467800	Enhancers	Hela-S3	cervix
33	chr6:142467400-142468000	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr6:142467400-142468000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
35	chr6:142467400-142468000	Flanking Active TSS	Dnd41	blood
36	chr6:142467400-142468800	Active TSS	Fetal Brain Male	brain
37	chr6:142467400-142469000	Active TSS	Brain Angular Gyrus	brain
38	chr6:142467400-142469000	Active TSS	Brain Hippocampus Middle	brain
39	chr6:142467400-142469000	Active TSS	Brain Inferior Temporal Lobe	brain
40	chr6:142467400-142469000	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr6:142467400-142469000	Active TSS	Fetal Lung	lung
42	chr6:142467400-142469200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:142467400-142469200	Active TSS	Colon Smooth Muscle	Colon
44	chr6:142467400-142469200	Active TSS	Rectal Mucosa Donor 29	rectum
45	chr6:142467400-142469200	Active TSS	Stomach Smooth Muscle	stomach

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