Variant report

Variant	rs11970705
Chromosome Location	chr6:11229953-11229954
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:11144154..11146594-chr6:11228087..11231091,3	MCF-7	breast:
2	chr6:11206157..11210739-chr6:11227507..11231085,4	MCF-7	breast:
3	chr6:11209074..11211031-chr6:11228787..11231392,2	MCF-7	breast:
4	chr6:11172565..11174594-chr6:11228822..11230575,2	MCF-7	breast:
5	chr6:11229014..11231620-chr6:11494391..11496101,2	MCF-7	breast:
6	chr6:11227633..11230379-chr6:11430461..11433425,2	MCF-7	breast:
7	chr6:11229690..11234119-chr6:11380884..11384431,5	MCF-7	breast:
8	chr6:11229128..11232149-chr6:11433876..11436826,3	MCF-7	breast:
9	chr6:11228247..11230066-chr6:11234822..11237148,2	MCF-7	breast:
10	chr6:11227854..11232586-chr6:11280753..11285913,6	MCF-7	breast:
11	chr6:11217430..11219520-chr6:11228784..11230869,3	MCF-7	breast:
12	chr6:11228618..11230806-chr6:11414420..11416664,2	MCF-7	breast:
13	chr6:11229798..11231566-chr6:11239902..11241851,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000247925	Chromatin interaction
ENSG00000111859	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs1475345	0.82[LWK][hapmap]
rs9380152	0.83[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][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	nsv1021078	chr6:10819083-11558560	Enhancers Strong transcription Active TSS Flanking Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases
2	nsv538135	chr6:10819083-11558560	Weak transcription Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	47 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11970705	TFAP2A	cis	cerebellum	SCAN
rs11970705	CCDC90A	cis	cerebellum	SCAN

Chromatin state (count:116 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:11215400-11232000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr6:11216600-11231800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr6:11220000-11230800	Weak transcription	Skeletal Muscle Female	skeletal muscle
4	chr6:11223200-11230600	Transcr. at gene 5' and 3'	HepG2	liver
5	chr6:11223400-11232000	Weak transcription	Pancreas	Pancrea
6	chr6:11225200-11231600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr6:11225200-11232200	Weak transcription	Gastric	stomach
8	chr6:11225400-11232200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr6:11225600-11230400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr6:11225600-11230600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr6:11225600-11231800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr6:11225800-11230400	Weak transcription	Primary T helper cells fromperipheralblood	blood
13	chr6:11225800-11230600	Weak transcription	Primary T cells from cord blood	blood
14	chr6:11225800-11231800	Weak transcription	Primary B cells from peripheral blood	blood
15	chr6:11226200-11230800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
16	chr6:11226200-11233600	Active TSS	Psoas Muscle	Psoas
17	chr6:11226400-11230400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr6:11226400-11230600	Weak transcription	Primary B cells from cord blood	blood
19	chr6:11226400-11230600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr6:11226400-11232600	Weak transcription	Spleen	Spleen
21	chr6:11226600-11233400	Active TSS	Right Atrium	heart
22	chr6:11227200-11230000	Enhancers	Fetal Heart	heart
23	chr6:11227400-11231800	Active TSS	Rectal Smooth Muscle	rectum
24	chr6:11227400-11231800	Active TSS	Skeletal Muscle Male	skeletal muscle
25	chr6:11227400-11233400	Active TSS	Left Ventricle	heart
26	chr6:11227600-11233600	Active TSS	Rectal Mucosa Donor 29	rectum
27	chr6:11228000-11230200	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr6:11228000-11230600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
29	chr6:11228000-11233400	Active TSS	Right Ventricle	heart
30	chr6:11228000-11233600	Active TSS	Lung	lung
31	chr6:11228800-11230200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
32	chr6:11228800-11230200	Flanking Active TSS	Adipose Nuclei	Adipose
33	chr6:11228800-11230200	Transcr. at gene 5' and 3'	Placenta Amnion	Placenta Amnion
34	chr6:11228800-11230200	Flanking Active TSS	NH-A	brain
35	chr6:11228800-11230800	Transcr. at gene 5' and 3'	A549	lung
36	chr6:11228800-11231800	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
37	chr6:11228800-11231800	Active TSS	Duodenum Smooth Muscle	Duodenum
38	chr6:11228800-11232000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
39	chr6:11228800-11233400	Active TSS	Brain Anterior Caudate	brain
40	chr6:11228800-11233600	Active TSS	Pancreatic Islets	Pancreatic Islet
41	chr6:11229000-11230000	Enhancers	H1 Cell Line	embryonic stem cell
42	chr6:11229000-11230200	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
43	chr6:11229000-11231400	Flanking Active TSS	HUVEC	blood vessel
44	chr6:11229000-11233200	Active TSS	Fetal Brain Female	brain
45	chr6:11229000-11233600	Active TSS	Colonic Mucosa	Colon
46	chr6:11229000-11233600	Active TSS	Fetal Stomach	stomach
47	chr6:11229000-11233600	Active TSS	NHLF	lung
48	chr6:11229000-11234200	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr6:11229200-11230000	Flanking Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr6:11229200-11230000	Flanking Active TSS	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links