Variant report

Variant	rs4902254
Chromosome Location	chr14:64395569-64395570
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10873172	0.82[CHB][hapmap]
rs11158521	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11621026	0.81[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11623256	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12878312	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17101465	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35539333	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4899122	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4899123	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs55989826	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs56028641	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56259838	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7155075	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv915909	chr14:63620440-64560369	Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	67 gene(s)	inside rSNPs	diseases
2	nsv1038825	chr14:64109441-64491720	Enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	34 gene(s)	inside rSNPs	diseases
3	nsv1037140	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv542119	chr14:64248421-64442980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv564904	chr14:64346190-64416898	Weak transcription Genic enhancers Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv1793389	chr14:64346190-64457224	Enhancers Flanking Active TSS Weak transcription Active TSS Strong transcription Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
7	nsv902019	chr14:64395569-64882380	Enhancers Strong transcription Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4902254	C14orf39	cis	cerebellum	SCAN
rs4902254	SYNE2	cis	cerebellum	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64337800-64403800	Weak transcription	Thymus	Thymus
2	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
3	chr14:64374600-64399600	Weak transcription	HUES48 Cell Line	embryonic stem cell
4	chr14:64376000-64399200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
5	chr14:64376000-64399600	Weak transcription	Small Intestine	intestine
6	chr14:64376000-64399800	Weak transcription	Primary T cells from cord blood	blood
7	chr14:64376000-64416200	Weak transcription	Skeletal Muscle Female	skeletal muscle
8	chr14:64376200-64399400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
9	chr14:64378000-64404800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr14:64378000-64416200	Weak transcription	Fetal Lung	lung
11	chr14:64378400-64416000	Weak transcription	Primary B cells from cord blood	blood
12	chr14:64378800-64401200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr14:64379800-64409000	Weak transcription	Fetal Muscle Trunk	muscle
14	chr14:64384200-64399600	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr14:64385600-64395600	Weak transcription	Ovary	ovary
16	chr14:64386400-64403800	Weak transcription	Esophagus	oesophagus
17	chr14:64386400-64405600	Weak transcription	Pancreas	Pancrea
18	chr14:64386600-64403400	Weak transcription	Gastric	stomach
19	chr14:64387000-64404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr14:64387000-64416400	Weak transcription	Aorta	Aorta
21	chr14:64387200-64396600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:64387200-64399800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr14:64387400-64396400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr14:64387400-64399800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr14:64390000-64399200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr14:64390200-64398400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:64390200-64398600	Weak transcription	Primary T helper cells PMA-I stimulated	--
28	chr14:64390200-64399400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr14:64390200-64399400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
30	chr14:64390200-64399400	Weak transcription	Duodenum Mucosa	Duodenum
31	chr14:64390200-64400600	Weak transcription	Right Atrium	heart
32	chr14:64390200-64416400	Weak transcription	Skeletal Muscle Male	skeletal muscle
33	chr14:64390400-64399400	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr14:64390400-64399400	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr14:64390600-64399600	Weak transcription	NHEK	skin
36	chr14:64390600-64418800	Weak transcription	HepG2	liver
37	chr14:64390800-64399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr14:64390800-64399400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr14:64390800-64399600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
40	chr14:64390800-64399600	Weak transcription	Stomach Mucosa	stomach
41	chr14:64390800-64404000	Weak transcription	Placenta	Placenta
42	chr14:64390800-64408600	Weak transcription	Fetal Intestine Large	intestine
43	chr14:64391000-64400000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
44	chr14:64391600-64399400	Weak transcription	Primary T helper cells fromperipheralblood	blood
45	chr14:64392000-64399400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr14:64392000-64405600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr14:64392000-64409000	Weak transcription	Fetal Intestine Small	intestine
48	chr14:64392200-64399600	Weak transcription	Brain Germinal Matrix	brain
49	chr14:64393200-64419800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
50	chr14:64393600-64399400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links