Variant report

Variant	rs2775001
Chromosome Location	chr14:64416814-64416815
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 63 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11621026	0.81[CHD][hapmap]
rs11624124	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11844554	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11850427	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1255855	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1255858	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1255859	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1255860	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1255861	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs1255862	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255863	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255864	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1255865	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255866	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255868	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1255870	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1255886	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1255889	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255893	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255894	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1255895	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255897	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255899	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255904	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255906	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255907	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255909	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1255911	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1255912	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1262234	0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1262236	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1273191	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1273193	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2094834	0.82[AMR][1000 genomes]
rs2275019	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2775000	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2775004	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2781426	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2781427	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2792207	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2884112	0.83[AFR][1000 genomes];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2884113	0.86[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4027383	0.92[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4027384	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4902253	0.81[CEU][hapmap]
rs61984086	0.82[EUR][1000 genomes]
rs7142401	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156778	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7159878	0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7161272	0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs8010312	0.92[CEU][hapmap]
rs8022079	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs8022635	0.85[EUR][1000 genomes]
rs945025	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs945029	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs946916	0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2775001	C14orf39	cis	cerebellum	SCAN

Chromatin state (count:99 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:64365000-64430200	Weak transcription	Fetal Brain Male	brain
2	chr14:64390600-64418800	Weak transcription	HepG2	liver
3	chr14:64393200-64419800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr14:64395000-64491000	Weak transcription	Psoas Muscle	Psoas
5	chr14:64396000-64418600	Weak transcription	Fetal Heart	heart
6	chr14:64400000-64419800	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr14:64400800-64417800	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr14:64401400-64430200	Weak transcription	Stomach Mucosa	stomach
9	chr14:64401600-64427800	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr14:64403600-64432800	Weak transcription	Lung	lung
11	chr14:64405000-64423400	Weak transcription	HSMM	muscle
12	chr14:64405600-64418800	Weak transcription	HMEC	breast
13	chr14:64405800-64418800	Weak transcription	Small Intestine	intestine
14	chr14:64406200-64434400	Weak transcription	Hela-S3	cervix
15	chr14:64407200-64418800	Weak transcription	HUVEC	blood vessel
16	chr14:64408200-64432000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr14:64408400-64430200	Weak transcription	Pancreatic Islets	Pancreatic Islet
18	chr14:64409000-64417800	Weak transcription	HUES48 Cell Line	embryonic stem cell
19	chr14:64410000-64417600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr14:64410000-64418400	Weak transcription	HUES64 Cell Line	embryonic stem cell
21	chr14:64410000-64422800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
22	chr14:64410000-64429600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr14:64411200-64424600	Strong transcription	Primary T cells fromperipheralblood	blood
24	chr14:64411800-64425200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
25	chr14:64412200-64419000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr14:64414400-64439600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr14:64414800-64418000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr14:64415400-64417400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr14:64415400-64418600	Weak transcription	NHLF	lung
30	chr14:64415400-64435800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr14:64415600-64418800	Strong transcription	Primary T helper cells PMA-I stimulated	--
32	chr14:64415600-64419200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr14:64415600-64419400	Strong transcription	Primary neutrophils fromperipheralblood	blood
34	chr14:64415600-64425400	Strong transcription	Dnd41	blood
35	chr14:64415600-64439000	Weak transcription	Stomach Smooth Muscle	stomach
36	chr14:64415800-64417400	Strong transcription	Primary T killer memory cells from peripheral blood	blood
37	chr14:64416000-64417000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
38	chr14:64416000-64418800	Strong transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr14:64416000-64419000	Strong transcription	Primary B cells from cord blood	blood
40	chr14:64416000-64419200	Strong transcription	Fetal Stomach	stomach
41	chr14:64416000-64421600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
42	chr14:64416200-64417000	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
43	chr14:64416200-64417000	Strong transcription	Colon Smooth Muscle	Colon
44	chr14:64416200-64417000	Strong transcription	Ovary	ovary
45	chr14:64416200-64417000	Strong transcription	NHEK	skin
46	chr14:64416200-64417200	Strong transcription	Esophagus	oesophagus
47	chr14:64416200-64417400	Strong transcription	Primary B cells from peripheral blood	blood
48	chr14:64416200-64417400	Strong transcription	Right Ventricle	heart
49	chr14:64416200-64417600	Strong transcription	Primary T helper naive cells from peripheral blood	blood
50	chr14:64416200-64417600	Strong transcription	Fetal Lung	lung

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links