Variant report

Variant	rs669009
Chromosome Location	chr6:150387302-150387303
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:150386654..150388325-chr6:150388815..150391248,2	MCF-7	breast:
2	chr6:150354931..150357925-chr6:150386556..150388661,2	K562	blood:
3	chr6:150345687..150347890-chr6:150385680..150387900,2	MCF-7	breast:
4	chr6:150378922..150380433-chr6:150385877..150388167,2	K562	blood:

Variant related genes	Relation type
ENSG00000155918	Chromatin interaction
ENSG00000131019	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs1853659	0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2010440	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4038366	0.83[EUR][1000 genomes]
rs4869814	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870250	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4870258	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.91[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4870272	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs599319	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610025	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs610039	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs631796	0.81[EUR][1000 genomes]
rs6557277	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6557278	0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6920662	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6933841	0.91[CEU][hapmap];1.00[CHB][hapmap];0.83[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6935471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7747128	0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs7760655	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs789830	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs9322241	0.81[EUR][1000 genomes]
rs945194	0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9479408	0.83[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv886764	chr6:150114745-150393683	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases
2	nsv517022	chr6:150145001-150426272	Bivalent Enhancer Weak transcription Flanking Bivalent TSS/Enh Strong transcription Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	39 gene(s)	inside rSNPs	diseases
3	esv7375	chr6:150324114-150388625	Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
4	esv3344440	chr6:150324131-150388650	Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
5	esv3323918	chr6:150327978-150392099	Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
6	nsv886767	chr6:150335407-150400488	Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Active TSS Strong transcription Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
7	nsv1026236	chr6:150360882-150408946	Flanking Active TSS Enhancers Active TSS Weak transcription ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:150376000-150388800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
2	chr6:150377800-150389400	Weak transcription	HSMMtube	muscle
3	chr6:150378600-150389400	Weak transcription	Right Atrium	heart
4	chr6:150379600-150389200	Weak transcription	Hela-S3	cervix
5	chr6:150380000-150389600	Weak transcription	Aorta	Aorta
6	chr6:150380200-150389400	Weak transcription	HSMM	muscle
7	chr6:150380600-150389200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
8	chr6:150380800-150387800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
9	chr6:150380800-150389200	Weak transcription	HMEC	breast
10	chr6:150380800-150389400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr6:150381000-150389200	Weak transcription	Lung	lung
12	chr6:150381400-150389200	Weak transcription	Cortex derived primary cultured neurospheres	brain
13	chr6:150381600-150389200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr6:150381600-150389200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr6:150381600-150389200	Weak transcription	Right Ventricle	heart
16	chr6:150381600-150389400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:150381600-150389400	Weak transcription	Primary hematopoietic stem cells	blood
18	chr6:150381800-150389200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:150381800-150389200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr6:150381800-150389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr6:150382000-150389200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr6:150382000-150389200	Weak transcription	Esophagus	oesophagus
23	chr6:150382200-150389200	Weak transcription	Pancreas	Pancrea
24	chr6:150382600-150389400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr6:150382800-150389400	Weak transcription	NH-A	brain
26	chr6:150383000-150389200	Weak transcription	NHLF	lung
27	chr6:150383200-150389400	Weak transcription	Fetal Brain Female	brain
28	chr6:150383800-150389200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
29	chr6:150383800-150389400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr6:150384000-150389400	Weak transcription	Brain Inferior Temporal Lobe	brain
31	chr6:150384600-150387400	Strong transcription	Fetal Stomach	stomach
32	chr6:150384800-150389400	Weak transcription	Fetal Kidney	kidney
33	chr6:150385000-150389400	Weak transcription	Fetal Lung	lung
34	chr6:150385200-150389400	Weak transcription	Ovary	ovary
35	chr6:150385800-150389200	Weak transcription	Fetal Muscle Trunk	muscle
36	chr6:150386400-150388200	Weak transcription	Fetal Intestine Small	intestine
37	chr6:150386600-150388400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr6:150386600-150389600	Weak transcription	NHEK	skin
39	chr6:150386800-150388400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
40	chr6:150386800-150389200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr6:150387000-150389000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr6:150387000-150389200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr6:150387000-150389200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr6:150387000-150389200	Weak transcription	Muscle Satellite Cultured Cells	--
45	chr6:150387000-150389200	Weak transcription	Osteobl	bone
46	chr6:150387000-150389400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
47	chr6:150387000-150389600	Weak transcription	Gastric	stomach
48	chr6:150387200-150388200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
49	chr6:150387200-150389200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr6:150387200-150389200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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