Variant report

Variant	rs7142401
Chromosome Location	chr14:64472722-64472723
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11621026	0.81[ASW][hapmap]
rs11624124	0.83[EUR][1000 genomes]
rs11844554	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11850427	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255855	0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1255858	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255859	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255860	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255861	0.91[EUR][1000 genomes]
rs1255862	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255863	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255864	0.92[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255865	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255866	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255868	0.85[EUR][1000 genomes]
rs1255870	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255886	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255889	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255893	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255894	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1255895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255897	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255898	0.81[EUR][1000 genomes]
rs1255899	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255904	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255906	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255907	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255909	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255911	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1255912	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1262234	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1262236	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1273191	0.80[ASN][1000 genomes]
rs1273193	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2275019	0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2775000	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2775001	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2775004	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2781426	0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2781427	0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2792207	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2884112	0.80[ASN][1000 genomes]
rs2884113	0.87[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs4027383	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4027384	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7156778	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7159878	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];0.96[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7161272	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8010312	0.84[CEU][hapmap]
rs8022079	0.83[EUR][1000 genomes]
rs8022635	0.90[EUR][1000 genomes]
rs945025	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs945029	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs946916	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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	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
4	nsv456326	chr14:64420413-64754361	Strong transcription Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
5	nsv564905	chr14:64420413-64754361	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	6 gene(s)	inside rSNPs	diseases
6	nsv902020	chr14:64434288-64506541	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7142401	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
2	chr14:64419200-64489000	Weak transcription	Small Intestine	intestine
3	chr14:64440800-64480400	Strong transcription	Primary T cells fromperipheralblood	blood
4	chr14:64442400-64491000	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr14:64452400-64480600	Strong transcription	Primary T helper cells fromperipheralblood	blood
6	chr14:64452600-64479200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
7	chr14:64457000-64474600	Strong transcription	Primary T helper cells PMA-I stimulated	--
8	chr14:64457000-64480000	Strong transcription	Dnd41	blood
9	chr14:64457000-64502000	Strong transcription	Placenta	Placenta
10	chr14:64457000-64519200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
11	chr14:64457200-64476000	Strong transcription	Fetal Brain Female	brain
12	chr14:64457200-64480200	Strong transcription	Primary neutrophils fromperipheralblood	blood
13	chr14:64458800-64490400	Weak transcription	Colonic Mucosa	Colon
14	chr14:64459600-64478800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr14:64459600-64481200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr14:64460000-64481200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:64460000-64488000	Weak transcription	Pancreas	Pancrea
18	chr14:64460000-64513400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:64460600-64495000	Weak transcription	NHDF-Ad	bronchial
20	chr14:64462200-64473000	Strong transcription	Rectal Mucosa Donor 31	rectum
21	chr14:64462600-64475800	Strong transcription	Fetal Intestine Large	intestine
22	chr14:64462600-64479000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
23	chr14:64462600-64479000	Strong transcription	Fetal Stomach	stomach
24	chr14:64462800-64472800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
25	chr14:64462800-64476000	Strong transcription	Rectal Mucosa Donor 29	rectum
26	chr14:64462800-64476200	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
27	chr14:64463200-64491000	Weak transcription	Fetal Brain Male	brain
28	chr14:64463600-64475000	Strong transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:64464000-64488600	Weak transcription	HUVEC	blood vessel
30	chr14:64464800-64474000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr14:64465800-64475600	Strong transcription	Cortex derived primary cultured neurospheres	brain
32	chr14:64466400-64490600	Weak transcription	H1 Cell Line	embryonic stem cell
33	chr14:64466600-64473800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
34	chr14:64466600-64490400	Weak transcription	Rectal Smooth Muscle	rectum
35	chr14:64466600-64513200	Weak transcription	NHEK	skin
36	chr14:64466600-64593200	Weak transcription	Colon Smooth Muscle	Colon
37	chr14:64466800-64474000	Weak transcription	Fetal Heart	heart
38	chr14:64467800-64475800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:64468000-64475600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
40	chr14:64468000-64480600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr14:64468400-64482200	Weak transcription	Pancreatic Islets	Pancreatic Islet
42	chr14:64468800-64527200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
43	chr14:64469200-64488000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
44	chr14:64469400-64475600	Strong transcription	Brain Germinal Matrix	brain
45	chr14:64469600-64475600	Strong transcription	Duodenum Mucosa	Duodenum
46	chr14:64469600-64518400	Weak transcription	HMEC	breast
47	chr14:64470000-64490600	Weak transcription	Placenta Amnion	Placenta Amnion
48	chr14:64470200-64475600	Strong transcription	Thymus	Thymus
49	chr14:64470200-64488000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
50	chr14:64470400-64474000	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links