Variant report

Variant	rs2039907
Chromosome Location	chr6:4930772-4930773
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:4929125..4930860-chr6:4939699..4942509,2	MCF-7	breast:
2	chr6:4927539..4929296-chr6:4930771..4933089,2	K562	blood:
3	chr6:4927539..4929623-chr6:4930066..4933089,3	K562	blood:

Variant related genes	Relation type
ENSG00000153046	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs13208366	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1341093	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1341094	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1539002	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1539003	0.99[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2027418	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2039906	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3804547	0.83[EUR][1000 genomes]
rs6911199	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6911937	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6922170	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7743681	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9378921	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9392642	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1023527	chr6:4729592-5387176	Strong transcription Weak transcription Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	esv2422499	chr6:4745428-5073222	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	18 gene(s)	inside rSNPs	diseases
3	nsv830577	chr6:4834567-5050544	Enhancers Weak transcription Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv462622	chr6:4904380-5172009	Active TSS Enhancers Strong transcription Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	19 gene(s)	inside rSNPs	diseases
5	nsv600871	chr6:4904380-5172009	Enhancers Active TSS Flanking Active TSS Weak transcription ZNF genes & repeats Strong transcription 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 miRNA target site	19 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:4905800-4931200	Weak transcription	HepG2	liver
2	chr6:4908000-4935600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
3	chr6:4908200-4934800	Weak transcription	Primary B cells from cord blood	blood
4	chr6:4911000-4935200	Weak transcription	Primary monocytes fromperipheralblood	blood
5	chr6:4912800-4931200	Weak transcription	Rectal Mucosa Donor 29	rectum
6	chr6:4913200-4936000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:4913200-4941000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
8	chr6:4913600-4938000	Weak transcription	Primary B cells from peripheral blood	blood
9	chr6:4915200-4931600	Weak transcription	Esophagus	oesophagus
10	chr6:4915400-4931000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:4915400-4931800	Weak transcription	Pancreas	Pancrea
12	chr6:4915600-4931200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr6:4915600-4931200	Weak transcription	NHEK	skin
14	chr6:4915800-4931600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
15	chr6:4915800-4942400	Weak transcription	Aorta	Aorta
16	chr6:4916200-4933200	Weak transcription	Fetal Stomach	stomach
17	chr6:4916600-4935400	Weak transcription	Monocytes-CD14+_RO01746	blood
18	chr6:4917000-4931400	Weak transcription	Fetal Intestine Small	intestine
19	chr6:4917200-4935000	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr6:4918000-4936000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr6:4921200-4931600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr6:4922600-4931600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr6:4923000-4931800	Weak transcription	Spleen	Spleen
24	chr6:4923000-4937800	Weak transcription	Primary T cells from cord blood	blood
25	chr6:4924600-4931600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr6:4925400-4934800	Weak transcription	GM12878-XiMat	blood
27	chr6:4925600-4930800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr6:4925600-4941600	Weak transcription	Primary hematopoietic stem cells	blood
29	chr6:4926400-4931200	Weak transcription	Skeletal Muscle Male	skeletal muscle
30	chr6:4926800-4931200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
31	chr6:4927600-4940200	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr6:4928200-4931800	Enhancers	HSMM	muscle
33	chr6:4928200-4933600	Enhancers	HSMMtube	muscle
34	chr6:4928400-4932000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr6:4928600-4932800	Enhancers	ES-WA7 Cell Line	embryonic stem cell
36	chr6:4928800-4931600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:4928800-4933200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
38	chr6:4928800-4935600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
39	chr6:4929000-4931600	Weak transcription	HMEC	breast
40	chr6:4929200-4931600	Weak transcription	NHDF-Ad	bronchial
41	chr6:4929200-4932400	Enhancers	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr6:4929400-4931800	Enhancers	K562	blood
43	chr6:4929400-4932600	Enhancers	Fetal Heart	heart
44	chr6:4929400-4941600	Weak transcription	Osteobl	bone
45	chr6:4929600-4931400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
46	chr6:4929600-4931800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr6:4929600-4931800	Weak transcription	Muscle Satellite Cultured Cells	--
48	chr6:4929600-4931800	Weak transcription	NHLF	lung
49	chr6:4929600-4932800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:4929800-4931200	Enhancers	Hela-S3	cervix

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