Variant report

Variant	rs2878172
Chromosome Location	chr14:55373670-55373671
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 77 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:73)

rs_ID	r²[population]
rs1002054	0.81[JPT][hapmap]
rs10131232	0.83[YRI][hapmap]
rs10133650	0.86[YRI][hapmap]
rs10133662	0.81[YRI][hapmap]
rs10136972	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10137071	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs10140164	0.87[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10145268	0.81[JPT][hapmap]
rs10149103	0.86[ASN][1000 genomes]
rs1107960	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs11158028	0.92[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11621165	0.91[CHB][hapmap];0.92[JPT][hapmap];0.86[ASN][1000 genomes]
rs11621177	0.86[ASN][1000 genomes]
rs11626396	0.86[ASN][1000 genomes]
rs11846809	0.85[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs11847771	0.92[CHB][hapmap]
rs11852045	0.84[ASN][1000 genomes]
rs1187877	0.81[JPT][hapmap]
rs1187883	0.85[JPT][hapmap]
rs1201378	0.81[JPT][hapmap]
rs1209087	0.81[JPT][hapmap]
rs12147796	0.86[ASN][1000 genomes]
rs13379159	0.81[JPT][hapmap]
rs17128052	0.83[CHB][hapmap]
rs17128120	0.87[ASW][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap]
rs17253633	0.85[JPT][hapmap]
rs17832269	0.80[ASN][1000 genomes]
rs17832311	0.81[JPT][hapmap]
rs2149482	1.00[ASN][1000 genomes]
rs2183081	0.88[YRI][hapmap]
rs2251366	0.81[JPT][hapmap]
rs28481699	0.86[ASN][1000 genomes]
rs2878174	0.87[ASW][hapmap];0.80[CEU][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.82[TSI][hapmap]
rs3742564	0.81[JPT][hapmap]
rs3759664	0.83[CHB][hapmap];0.92[JPT][hapmap];0.82[ASN][1000 genomes]
rs3759665	0.82[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs3783641	0.92[CHB][hapmap]
rs3783642	0.80[ASW][hapmap];1.00[CEU][hapmap];0.81[GIH][hapmap];0.80[LWK][hapmap];0.95[MEX][hapmap];0.94[MKK][hapmap];0.95[TSI][hapmap];0.96[YRI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs3783644	0.80[ASN][1000 genomes]
rs4335711	0.85[JPT][hapmap]
rs56164809	0.91[ASN][1000 genomes]
rs60258834	0.82[ASN][1000 genomes]
rs61224609	0.88[ASN][1000 genomes]
rs6572993	0.80[ASN][1000 genomes]
rs6572994	0.82[ASN][1000 genomes]
rs6572999	0.81[JPT][hapmap]
rs7144602	0.83[YRI][hapmap]
rs7144652	0.80[JPT][hapmap]
rs7146285	0.87[ASW][hapmap];0.85[CHB][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs7147201	0.92[CHB][hapmap]
rs7147286	0.96[YRI][hapmap]
rs7152033	0.89[ASN][1000 genomes]
rs7153937	0.85[JPT][hapmap]
rs8005399	0.81[JPT][hapmap]
rs8006363	0.84[ASN][1000 genomes]
rs8007201	0.88[YRI][hapmap]
rs8007267	0.92[CHB][hapmap];0.92[JPT][hapmap];0.88[YRI][hapmap];0.86[ASN][1000 genomes]
rs8008858	0.85[ASN][1000 genomes]
rs8009997	0.80[ASN][1000 genomes]
rs8011446	0.80[ASN][1000 genomes]
rs8012152	0.87[ASW][hapmap];0.92[CHD][hapmap];0.89[GIH][hapmap];0.93[JPT][hapmap];0.82[ASN][1000 genomes]
rs8012156	0.81[JPT][hapmap]
rs8013521	0.82[ASN][1000 genomes]
rs8017210	0.92[CHB][hapmap]
rs8018688	0.82[ASN][1000 genomes]
rs8019390	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[ASN][1000 genomes]
rs8019824	0.95[ASN][1000 genomes]
rs8020545	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs8021303	0.85[AMR][1000 genomes];0.82[ASN][1000 genomes]
rs8022049	0.87[CHD][hapmap];0.93[JPT][hapmap]
rs8022453	0.92[CHB][hapmap];0.92[JPT][hapmap];0.84[ASN][1000 genomes]
rs8023187	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.97[ASN][1000 genomes]
rs9285583	0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530042	chr14:55208170-55386966	Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
2	nsv932970	chr14:55326559-55532749	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
3	esv3358123	chr14:55359251-55378030	Flanking Active TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Weak transcription Bivalent Enhancer Strong transcription Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	n/a
4	nsv68444	chr14:55373670-55373671	Weak transcription Bivalent Enhancer Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	n/a

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2878172	ATG14	cis	parietal	SCAN
rs2878172	FBXO34	cis	cerebellum	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55370200-55374600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr14:55370200-55374800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
3	chr14:55370200-55376800	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr14:55370400-55374400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr14:55370400-55374600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr14:55370400-55374600	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr14:55370400-55374600	Weak transcription	Dnd41	blood
8	chr14:55370400-55374800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr14:55370400-55374800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr14:55370600-55374600	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr14:55370600-55388600	Weak transcription	HepG2	liver
12	chr14:55372200-55373800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr14:55372200-55374600	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr14:55372200-55374800	Weak transcription	Primary monocytes fromperipheralblood	blood
15	chr14:55373200-55374400	Weak transcription	GM12878-XiMat	blood
16	chr14:55373600-55373800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
17	chr14:55373600-55374000	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived

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