Variant report

Variant	rs2294746
Chromosome Location	chr6:29521676-29521677
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:29520442..29521980-chr6:29599358..29601313,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204681	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs11970406	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11970429	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11970475	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16895067	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs16895070	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17184255	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076484	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076486	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2076487	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2272991	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2294744	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57241384	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59731351	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59802757	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs64036	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6456964	0.96[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6913746	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs6915177	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73402729	0.87[EUR][1000 genomes]
rs73402731	0.81[EUR][1000 genomes]
rs73402733	0.87[EUR][1000 genomes]
rs7757931	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461536	0.84[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9461538	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9468551	0.94[EUR][1000 genomes]
rs9501677	0.89[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758039	chr6:29469101-29672665	Flanking Active TSS Active TSS Strong transcription Enhancers Weak transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
2	esv2759411	chr6:29469101-29672665	Active TSS Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:102 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29520400-29522000	Bivalent/Poised TSS	iPS-20b Cell Line	embryonic stem cell
2	chr6:29520600-29521800	Flanking Bivalent TSS/Enh	Primary B cells from peripheral blood	blood
3	chr6:29520600-29521800	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
4	chr6:29520600-29521800	Flanking Bivalent TSS/Enh	Primary T regulatory cells fromperipheralblood	blood
5	chr6:29520600-29521800	Bivalent Enhancer	Cortex derived primary cultured neurospheres	brain
6	chr6:29520600-29521800	Bivalent/Poised TSS	Rectal Mucosa Donor 29	rectum
7	chr6:29520600-29521800	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
8	chr6:29520600-29521800	Flanking Bivalent TSS/Enh	Skeletal Muscle Female	skeletal muscle
9	chr6:29520600-29522000	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
10	chr6:29520600-29522000	Bivalent Enhancer	Stomach Mucosa	stomach
11	chr6:29520600-29522000	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
12	chr6:29520600-29522200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
13	chr6:29520600-29522200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
14	chr6:29520600-29522200	Bivalent Enhancer	Fetal Stomach	stomach
15	chr6:29520600-29522200	Bivalent Enhancer	Fetal Thymus	thymus
16	chr6:29520800-29521800	Flanking Bivalent TSS/Enh	Primary mononuclear cells fromperipheralblood	Blood
17	chr6:29520800-29521800	Flanking Bivalent TSS/Enh	Duodenum Smooth Muscle	Duodenum
18	chr6:29520800-29521800	Bivalent Enhancer	Fetal Brain Male	brain
19	chr6:29520800-29521800	Bivalent/Poised TSS	Pancreatic Islets	Pancreatic Islet
20	chr6:29520800-29521800	Bivalent Enhancer	Placenta Amnion	Placenta Amnion
21	chr6:29520800-29522000	Bivalent/Poised TSS	ES-I3 Cell Line	embryonic stem cell
22	chr6:29520800-29522000	Bivalent/Poised TSS	H9 Cell Line	embryonic stem cell
23	chr6:29520800-29522000	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
24	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	ES-UCSF4 Cell Line	embryonic stem cell
25	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Primary T cells from cord blood	blood
26	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells short term culture	blood
27	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
30	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Foreskin Melanocyte Primary Cells skin03	Skin
32	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Brain Cingulate Gyrus	brain
33	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
34	chr6:29521000-29521800	Flanking Active TSS	Esophagus	oesophagus
35	chr6:29521000-29521800	Bivalent/Poised TSS	Fetal Brain Female	brain
36	chr6:29521000-29521800	Bivalent Enhancer	Placenta	Placenta
37	chr6:29521000-29521800	Enhancers	Ovary	ovary
38	chr6:29521000-29521800	Flanking Active TSS	Pancreas	Pancrea
39	chr6:29521000-29521800	Flanking Active TSS	Right Ventricle	heart
40	chr6:29521000-29521800	Bivalent/Poised TSS	Thymus	Thymus
41	chr6:29521000-29521800	Flanking Bivalent TSS/Enh	HMEC	breast
42	chr6:29521000-29522000	Flanking Bivalent TSS/Enh	iPS DF 19.11 Cell Line	embryonic stem cell
43	chr6:29521000-29522000	Flanking Bivalent TSS/Enh	Breast Myoepithelial Primary Cells	Breast
44	chr6:29521000-29522000	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
45	chr6:29521000-29522000	Bivalent Enhancer	Fetal Muscle Trunk	muscle
46	chr6:29521000-29522000	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
47	chr6:29521000-29522000	Bivalent Enhancer	Small Intestine	intestine
48	chr6:29521000-29522200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
49	chr6:29521000-29522200	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr6:29521200-29521800	Bivalent/Poised TSS	H1 Cell Line	embryonic stem cell

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