Variant report

Variant	rs9258253
Chromosome Location	chr6:29721532-29721533
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:29710119..29712623-chr6:29721345..29723379,2	MCF-7	breast:
2	chr6:29719431..29722230-chr6:29728984..29731849,2	MCF-7	breast:
3	chr6:29709930..29711722-chr6:29720449..29722464,2	K562	blood:
4	chr6:29721433..29724421-chr6:29794290..29797232,2	MCF-7	breast:
5	chr6:29716316..29718223-chr6:29719581..29721724,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000204632	Chromatin interaction
ENSG00000273340	Chromatin interaction
ENSG00000214922	Chromatin interaction
ENSG00000199290	Chromatin interaction
ENSG00000229142	Chromatin interaction
ENSG00000270896	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs3906250	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9258000	0.88[EUR][1000 genomes]
rs9258130	0.82[EUR][1000 genomes]
rs9258132	0.82[EUR][1000 genomes]
rs9258249	0.84[EUR][1000 genomes]
rs9258271	0.84[EUR][1000 genomes]
rs9258276	0.84[EUR][1000 genomes]
rs9258286	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9258385	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9258390	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9258391	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9258474	1.00[AMR][1000 genomes]
rs9258475	1.00[AMR][1000 genomes]
rs9258489	1.00[AMR][1000 genomes]
rs9258492	1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:11 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv20940	chr6:29653954-29923410	Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
2	nsv428475	chr6:29659525-29763392	Strong transcription Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv428139	chr6:29659525-29892317	Bivalent Enhancer Active TSS Enhancers Flanking Active TSS Bivalent/Poised TSS Weak transcription Strong transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	41 gene(s)	inside rSNPs	diseases
4	nsv427749	chr6:29659525-29975144	Enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	53 gene(s)	inside rSNPs	diseases
5	nsv508397	chr6:29663132-29761448	Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Transcr. at gene 5' and 3' Enhancers Bivalent/Poised TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
6	esv1821077	chr6:29670915-29726207	Flanking Bivalent TSS/Enh Weak transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
7	esv1794141	chr6:29670915-29765814	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
8	nsv10809	chr6:29692573-29794119	Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
9	nsv883532	chr6:29703262-29814963	Flanking Active TSS Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	25 gene(s)	inside rSNPs	diseases
10	nsv883534	chr6:29708222-29724310	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Weak transcription 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	16 gene(s)	inside rSNPs	diseases
11	esv3441842	chr6:29715749-29942950	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Strong transcription Bivalent/Poised TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:29719600-29721800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
2	chr6:29719800-29721600	Active TSS	Brain Cingulate Gyrus	brain
3	chr6:29719800-29721600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
4	chr6:29719800-29721600	Active TSS	HSMMtube	muscle
5	chr6:29720200-29721600	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
6	chr6:29720200-29721600	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
7	chr6:29720200-29721600	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr6:29720200-29721600	Active TSS	Brain Inferior Temporal Lobe	brain
9	chr6:29720400-29721600	Active TSS	Stomach Smooth Muscle	stomach
10	chr6:29721000-29721600	Enhancers	Primary T cells from cord blood	blood
11	chr6:29721000-29721600	Bivalent Enhancer	Fetal Intestine Large	intestine
12	chr6:29721000-29721800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
13	chr6:29721000-29721800	Enhancers	Duodenum Mucosa	Duodenum
14	chr6:29721000-29723000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
15	chr6:29721000-29723200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr6:29721000-29723200	Weak transcription	Spleen	Spleen
17	chr6:29721000-29724200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr6:29721000-29725200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr6:29721200-29721600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr6:29721200-29721600	Enhancers	Primary monocytes fromperipheralblood	blood
21	chr6:29721200-29721600	Enhancers	Primary B cells from cord blood	blood
22	chr6:29721200-29721600	Enhancers	Primary B cells from peripheral blood	blood
23	chr6:29721200-29721600	Enhancers	Primary T helper naive cells from peripheral blood	blood
24	chr6:29721200-29721600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
25	chr6:29721200-29721600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr6:29721200-29721600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr6:29721200-29721600	Enhancers	Adipose Nuclei	Adipose
28	chr6:29721200-29721600	Enhancers	Brain Hippocampus Middle	brain
29	chr6:29721200-29721600	Enhancers	Duodenum Smooth Muscle	Duodenum
30	chr6:29721200-29721600	Bivalent Enhancer	Fetal Lung	lung
31	chr6:29721200-29721600	Enhancers	Rectal Mucosa Donor 29	rectum
32	chr6:29721200-29721600	Enhancers	Skeletal Muscle Female	skeletal muscle
33	chr6:29721200-29721600	Flanking Active TSS	GM12878-XiMat	blood
34	chr6:29721200-29721600	Flanking Active TSS	NHEK	skin
35	chr6:29721200-29721800	Enhancers	Primary T helper cells PMA-I stimulated	--
36	chr6:29721200-29721800	Enhancers	Primary T helper cells fromperipheralblood	blood
37	chr6:29721200-29721800	Enhancers	Primary T killer memory cells from peripheral blood	blood
38	chr6:29721200-29721800	Enhancers	Colon Smooth Muscle	Colon
39	chr6:29721200-29721800	Enhancers	Skeletal Muscle Male	skeletal muscle
40	chr6:29721200-29723200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
41	chr6:29721200-29723200	Weak transcription	H9 Cell Line	embryonic stem cell
42	chr6:29721200-29723200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr6:29721200-29723600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr6:29721400-29721600	Enhancers	HUES48 Cell Line	embryonic stem cell
45	chr6:29721400-29721600	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
46	chr6:29721400-29721600	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
47	chr6:29721400-29721600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
48	chr6:29721400-29721600	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:29721400-29721600	Bivalent Enhancer	Fetal Stomach	stomach
50	chr6:29721400-29721600	Flanking Active TSS	Hela-S3	cervix

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