Variant report

Variant	rs12893917
Chromosome Location	chr14:55921409-55921410
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:55920824..55921477-chr8:146175730..146176235,2	HCT-116	colon:

Variant related genes	Relation type
ENSG00000170631	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10129695	0.95[AMR][1000 genomes];0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10136199	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10140081	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12879787	0.82[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12879987	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12897716	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1953738	0.85[ASN][1000 genomes]
rs28714246	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs34509040	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4898866	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv901958	chr14:55822095-56045411	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv901960	chr14:55853724-56085130	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
3	nsv901961	chr14:55853724-56101879	Enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
4	nsv901962	chr14:55862956-56101879	Enhancers Flanking Bivalent TSS/Enh Strong transcription Active TSS Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	30 gene(s)	inside rSNPs	diseases
5	nsv901963	chr14:55871452-56085130	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
6	nsv901964	chr14:55871452-56101879	Enhancers Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
7	nsv564874	chr14:55879685-56027815	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
8	nsv1051564	chr14:55895610-56130788	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
9	nsv542103	chr14:55895610-56130788	Strong transcription Weak transcription Enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:90 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55912600-55922000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
2	chr14:55913600-55925000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
3	chr14:55920400-55921800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr14:55920400-55921800	Enhancers	HUES6 Cell Line	embryonic stem cell
5	chr14:55920400-55922000	Enhancers	Breast Myoepithelial Primary Cells	Breast
6	chr14:55920400-55922200	Enhancers	Fetal Heart	heart
7	chr14:55920400-55922200	Enhancers	Sigmoid Colon	Sigmoid Colon
8	chr14:55920600-55921600	Enhancers	iPS-20b Cell Line	embryonic stem cell
9	chr14:55920600-55921800	Enhancers	ES-I3 Cell Line	embryonic stem cell
10	chr14:55920600-55921800	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr14:55920600-55921800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr14:55920600-55921800	Flanking Active TSS	Duodenum Mucosa	Duodenum
13	chr14:55920600-55921800	Enhancers	NHLF	lung
14	chr14:55920600-55922000	Enhancers	Fetal Brain Male	brain
15	chr14:55920600-55922000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
16	chr14:55920600-55922400	Enhancers	HUES64 Cell Line	embryonic stem cell
17	chr14:55920600-55922400	Enhancers	Fetal Intestine Small	intestine
18	chr14:55920800-55921600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
19	chr14:55920800-55921600	Enhancers	HUES48 Cell Line	embryonic stem cell
20	chr14:55920800-55921600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
21	chr14:55920800-55921600	Flanking Active TSS	Colon Smooth Muscle	Colon
22	chr14:55920800-55921600	Enhancers	Fetal Lung	lung
23	chr14:55920800-55921800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:55920800-55921800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr14:55920800-55921800	Enhancers	Primary monocytes fromperipheralblood	blood
26	chr14:55920800-55921800	Enhancers	Primary hematopoietic stem cells short term culture	blood
27	chr14:55920800-55921800	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr14:55920800-55921800	Enhancers	Gastric	stomach
29	chr14:55920800-55921800	Flanking Active TSS	Rectal Smooth Muscle	rectum
30	chr14:55920800-55921800	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr14:55920800-55921800	Flanking Active TSS	A549	lung
32	chr14:55920800-55921800	Enhancers	HepG2	liver
33	chr14:55920800-55921800	Enhancers	NHDF-Ad	bronchial
34	chr14:55920800-55922000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr14:55920800-55922000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
36	chr14:55920800-55922000	Enhancers	Fetal Intestine Large	intestine
37	chr14:55920800-55922000	Flanking Active TSS	Hela-S3	cervix
38	chr14:55920800-55922200	Enhancers	Fetal Stomach	stomach
39	chr14:55921000-55921600	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr14:55921000-55921600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr14:55921000-55921600	Flanking Active TSS	Adipose Nuclei	Adipose
42	chr14:55921000-55921600	Flanking Active TSS	Ovary	ovary
43	chr14:55921000-55921800	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
44	chr14:55921000-55921800	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr14:55921000-55921800	Flanking Active TSS	Brain Hippocampus Middle	brain
46	chr14:55921000-55921800	Flanking Active TSS	Brain Substantia Nigra	brain
47	chr14:55921000-55921800	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
48	chr14:55921000-55921800	Enhancers	Fetal Muscle Leg	muscle
49	chr14:55921000-55921800	Enhancers	Fetal Thymus	thymus
50	chr14:55921000-55921800	Enhancers	Pancreas	Pancrea

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links