Variant report

Variant	rs11622189
Chromosome Location	chr14:24907859-24907860
allele	C/T
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:14)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:14 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24801605..24806320-chr14:24904693..24909744,5	K562	blood:
2	chr14:24777377..24780208-chr14:24906174..24908907,2	K562	blood:
3	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
4	chr14:24789439..24822082-chr14:24898039..24913135,99	MCF-7	breast:
5	chr14:24872891..24878220-chr14:24906746..24909504,4	MCF-7	breast:
6	chr14:24791358..24808812-chr14:24895309..24913599,55	K562	blood:
7	chr14:24865931..24867961-chr14:24906005..24908600,2	MCF-7	breast:
8	chr14:24864264..24865862-chr14:24905132..24908041,2	MCF-7	breast:
9	chr14:24738558..24740532-chr14:24907754..24910468,2	MCF-7	breast:
10	chr14:24710779..24713776-chr14:24905054..24908249,5	MCF-7	breast:
11	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
12	chr14:24781460..24810019-chr14:24892340..24914262,110	MCF-7	breast:
13	chr14:24710058..24711559-chr14:24906353..24908721,2	MCF-7	breast:
14	chr14:24774877..24777510-chr14:24906503..24909154,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000129465	Chromatin interaction
ENSG00000092330	Chromatin interaction
ENSG00000213903	Chromatin interaction
ENSG00000213906	Chromatin interaction
ENSG00000207141	Chromatin interaction
ENSG00000136305	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000258973	Chromatin interaction
ENSG00000100949	Chromatin interaction
ENSG00000272658	Chromatin interaction
ENSG00000129467	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12884912	0.80[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs12886673	1.00[ASW][hapmap];0.96[CEU][hapmap];0.92[CHB][hapmap];0.91[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.95[TSI][hapmap];0.93[YRI][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs12896086	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes]
rs12896093	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.87[YRI][hapmap];0.80[AMR][1000 genomes]
rs1956918	1.00[CEU][hapmap];0.85[CHD][hapmap];0.84[GIH][hapmap];0.87[JPT][hapmap];0.93[MEX][hapmap];0.87[TSI][hapmap]

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	nsv1041336	chr14:24726564-25527319	Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases
2	nsv542000	chr14:24726564-25527319	Genic enhancers Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	107 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11622189	TM9SF1	cis	cerebellum	SCAN
rs11622189	METT11D1	cis	parietal	SCAN
rs11622189	IRF9	cis	parietal	SCAN
rs11622189	SDR39U1	cis	lymphoblastoid	seeQTL
rs11622189	OR4K1	cis	parietal	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24900200-24911000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:24900600-24910600	Weak transcription	Pancreatic Islets	Pancreatic Islet
3	chr14:24901000-24908600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:24901400-24910200	Strong transcription	Aorta	Aorta
5	chr14:24901600-24909800	Weak transcription	Fetal Heart	heart
6	chr14:24901600-24910400	Strong transcription	Placenta Amnion	Placenta Amnion
7	chr14:24901800-24909000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:24901800-24910000	Strong transcription	Sigmoid Colon	Sigmoid Colon
9	chr14:24902000-24909200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr14:24902200-24909400	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
11	chr14:24902400-24908600	Strong transcription	HMEC	breast
12	chr14:24902400-24909400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr14:24902400-24909800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr14:24902400-24910200	Strong transcription	A549	lung
15	chr14:24902400-24910600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr14:24903000-24910000	Weak transcription	Psoas Muscle	Psoas
17	chr14:24903000-24910000	Strong transcription	NHEK	skin
18	chr14:24903400-24909600	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
19	chr14:24903800-24908600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr14:24903800-24909000	Strong transcription	Pancreas	Pancrea
21	chr14:24904000-24908200	Genic enhancers	Liver	Liver
22	chr14:24904200-24910200	Genic enhancers	Skeletal Muscle Female	skeletal muscle
23	chr14:24904400-24910400	Genic enhancers	Adipose Nuclei	Adipose
24	chr14:24904600-24908200	Genic enhancers	Skeletal Muscle Male	skeletal muscle
25	chr14:24904600-24910400	Strong transcription	Fetal Lung	lung
26	chr14:24904800-24910400	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr14:24905000-24908600	Strong transcription	Gastric	stomach
28	chr14:24905200-24908200	Genic enhancers	Left Ventricle	heart
29	chr14:24905400-24908000	Genic enhancers	Fetal Thymus	thymus
30	chr14:24905400-24910000	Genic enhancers	Primary monocytes fromperipheralblood	blood
31	chr14:24905400-24910600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr14:24905400-24910600	Strong transcription	HUES6 Cell Line	embryonic stem cell
33	chr14:24905400-24911000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
34	chr14:24905600-24908200	Genic enhancers	Right Ventricle	heart
35	chr14:24905800-24908000	Genic enhancers	Primary neutrophils fromperipheralblood	blood
36	chr14:24905800-24908600	Strong transcription	iPS-15b Cell Line	embryonic stem cell
37	chr14:24905800-24910600	Strong transcription	HSMM	muscle
38	chr14:24906000-24908800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr14:24906000-24908800	Strong transcription	NHDF-Ad	bronchial
40	chr14:24906000-24909200	Strong transcription	NH-A	brain
41	chr14:24906000-24909200	Strong transcription	NHLF	lung
42	chr14:24906000-24909400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr14:24906000-24909400	Strong transcription	Muscle Satellite Cultured Cells	--
44	chr14:24906000-24910000	Strong transcription	Fetal Intestine Small	intestine
45	chr14:24906000-24910200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr14:24906000-24910400	Strong transcription	Rectal Mucosa Donor 29	rectum
47	chr14:24906000-24910400	Strong transcription	Osteobl	bone
48	chr14:24906200-24908200	Transcr. at gene 5' and 3'	Monocytes-CD14+_RO01746	blood
49	chr14:24906200-24908600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
50	chr14:24906200-24909400	Strong transcription	Cortex derived primary cultured neurospheres	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links