Variant report

Variant	rs2228233
Chromosome Location	chr14:24839165-24839166
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:10)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

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

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr14:24839143-24839176	GM13976	blood:	n/a	n/a

No data

(count:10 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:24837984..24840011-chr14:24867757..24869920,2	K562	blood:
2	chr14:24833553..24839988-chr14:24894553..24902357,9	K562	blood:
3	chr14:24827418..24850855-chr14:24894884..24913772,127	MCF-7	breast:
4	chr14:24836714..24839783-chr14:24910555..24913487,3	K562	blood:
5	chr14:24796879..24804920-chr14:24831628..24840088,12	MCF-7	breast:
6	chr14:24816528..24849574-chr14:24893305..24914155,145	MCF-7	breast:
7	chr14:24837386..24841607-chr14:24843315..24846573,5	K562	blood:
8	chr14:24833867..24840783-chr14:24879585..24886299,12	MCF-7	breast:
9	chr14:24833707..24839988-chr14:24896546..24902736,10	K562	blood:
10	chr14:24838955..24840778-chr14:24849371..24851355,2	K562	blood:

No data

Variant related genes	Relation type
NFATC4	TF binding region
ENSG00000100445	Chromatin interaction
ENSG00000129467	Chromatin interaction
ENSG00000205978	Chromatin interaction
ENSG00000100441	Chromatin interaction
ENSG00000100968	Chromatin interaction
ENSG00000139899	Chromatin interaction

Extended variants
information (count: 4 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11848279	0.95[CHD][hapmap];0.85[GIH][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[ASN][1000 genomes]
rs8008583	0.95[CHD][hapmap];0.91[JPT][hapmap];0.87[MEX][hapmap];0.83[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	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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2228233	OR9G4	trans	parietal	SCAN
rs2228233	NFATC4	cis	cerebellum	SCAN
rs2228233	NFATC4	cis	lymphoblastoid	seeQTL
rs2228233	ADCY4	cis	cerebellum	SCAN
rs2228233	NYNRIN	cis	cerebellum	SCAN
rs2228233	DHRS1	cis	multi-tissue	Pritchard
rs2228233	OR6S1	cis	cerebellum	SCAN
rs2228233	RIPK3	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:24835200-24839200	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:24837800-24839800	Enhancers	Fetal Brain Male	brain
3	chr14:24838200-24839400	Flanking Active TSS	Stomach Smooth Muscle	stomach
4	chr14:24838200-24850200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr14:24838400-24839200	Transcr. at gene 5' and 3'	Osteobl	bone
6	chr14:24838400-24839600	Transcr. at gene 5' and 3'	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr14:24838400-24839600	Enhancers	Lung	lung
8	chr14:24838400-24843000	Weak transcription	Aorta	Aorta
9	chr14:24838400-24844400	Weak transcription	Esophagus	oesophagus
10	chr14:24838600-24839200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
11	chr14:24838600-24839200	Weak transcription	Gastric	stomach
12	chr14:24838600-24839400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr14:24838600-24839600	Enhancers	Colonic Mucosa	Colon
14	chr14:24838600-24839600	Strong transcription	Fetal Intestine Small	intestine
15	chr14:24838600-24839800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr14:24838600-24839800	Enhancers	Placenta	Placenta
17	chr14:24838600-24840000	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr14:24838600-24840000	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
19	chr14:24838600-24840000	Enhancers	Fetal Thymus	thymus
20	chr14:24838600-24840800	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr14:24838600-24841000	Genic enhancers	Cortex derived primary cultured neurospheres	brain
22	chr14:24838600-24841800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
23	chr14:24838600-24842200	Weak transcription	Primary B cells from cord blood	blood
24	chr14:24838600-24842600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr14:24838600-24844000	Weak transcription	Brain Hippocampus Middle	brain
26	chr14:24838600-24844200	Weak transcription	Spleen	Spleen
27	chr14:24838600-24845600	Weak transcription	Right Atrium	heart
28	chr14:24838600-24846600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr14:24838800-24839200	Active TSS	NHDF-Ad	bronchial
30	chr14:24838800-24839400	ZNF genes & repeats	Fetal Intestine Large	intestine
31	chr14:24838800-24839600	Weak transcription	Fetal Lung	lung
32	chr14:24838800-24839600	Enhancers	Fetal Muscle Leg	muscle
33	chr14:24838800-24839800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:24838800-24839800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
35	chr14:24838800-24839800	Enhancers	Duodenum Smooth Muscle	Duodenum
36	chr14:24838800-24840000	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr14:24838800-24840200	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr14:24838800-24840400	Weak transcription	HUES64 Cell Line	embryonic stem cell
39	chr14:24838800-24840600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr14:24838800-24840600	Weak transcription	Adipose Nuclei	Adipose
41	chr14:24838800-24840600	Weak transcription	HUVEC	blood vessel
42	chr14:24838800-24840800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr14:24838800-24841200	Weak transcription	Left Ventricle	heart
44	chr14:24838800-24841600	Weak transcription	HUES6 Cell Line	embryonic stem cell
45	chr14:24838800-24841600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr14:24838800-24841600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
47	chr14:24838800-24841600	Weak transcription	Colon Smooth Muscle	Colon
48	chr14:24838800-24841600	Weak transcription	Ovary	ovary
49	chr14:24838800-24841800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr14:24838800-24841800	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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