Variant report

Variant	rs1952085
Chromosome Location	chr14:55512273-55512274
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:55493972..55498765-chr14:55510765..55514879,5	K562	blood:
2	chr14:55509588..55512063-chr14:55512122..55515108,3	K562	blood:
3	chr14:55497119..55499887-chr14:55511946..55513977,2	MCF-7	breast:
4	chr14:55500393..55503713-chr14:55510224..55513637,3	K562	blood:
5	chr14:55504558..55506513-chr14:55512059..55513763,2	K562	blood:
6	chr14:55492422..55495780-chr14:55511028..55514664,4	MCF-7	breast:
7	chr14:55509907..55511424-chr14:55511623..55513423,2	MCF-7	breast:
8	chr14:55495289..55498964-chr14:55511770..55513714,3	K562	blood:

No data

Variant related genes	Relation type
ENSG00000180008	Chromatin interaction
ENSG00000198554	Chromatin interaction

Extended variants
information (count: 53 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs1002054	1.00[CHB][hapmap];0.87[JPT][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs10135721	0.85[ASN][1000 genomes]
rs10145170	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs10145268	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10220693	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11622128	0.85[JPT][hapmap]
rs11625204	0.86[JPT][hapmap]
rs11626816	0.86[JPT][hapmap]
rs11627884	0.86[JPT][hapmap]
rs11849090	0.92[AFR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11849878	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11851178	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1187873	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs1187874	0.86[JPT][hapmap]
rs1187876	1.00[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1187877	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.86[TSI][hapmap];0.89[ASN][1000 genomes]
rs1187878	1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1187882	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1201378	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1209087	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1212641	0.86[JPT][hapmap];0.81[ASN][1000 genomes]
rs13379159	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17128128	0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128132	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17128145	0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.92[TSI][hapmap];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17832311	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2147963	0.86[JPT][hapmap]
rs2251366	1.00[CHB][hapmap];0.87[JPT][hapmap];0.82[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2340943	0.82[ASN][1000 genomes]
rs3742564	0.96[CEU][hapmap];1.00[CHB][hapmap];0.96[CHD][hapmap];0.87[JPT][hapmap];0.80[MEX][hapmap];0.97[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55843949	0.82[ASN][1000 genomes]
rs56725788	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs60805089	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6572999	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6573000	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7141975	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7144652	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7149965	0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7150145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7151224	0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7151431	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7161656	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs748017	0.80[ASN][1000 genomes]
rs8005399	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.88[ASN][1000 genomes]
rs8008134	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8012156	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs8021929	0.85[ASN][1000 genomes]
rs8022238	0.83[ASN][1000 genomes]
rs8022405	0.90[ASN][1000 genomes]
rs9323278	0.88[ASN][1000 genomes]
rs9671895	0.86[JPT][hapmap]
rs9806049	1.00[CHB][hapmap];0.92[CHD][hapmap];0.81[JPT][hapmap];0.86[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1952085	FBXO34	cis	cerebellum	SCAN
rs1952085	WDHD1	cis	parietal	SCAN
rs1952085	RPL13AP3	cis	cerebellum	SCAN
rs1952085	ATG14	cis	parietal	SCAN

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55494400-55517600	Weak transcription	Lung	lung
2	chr14:55495000-55517600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr14:55495000-55517600	Weak transcription	Esophagus	oesophagus
4	chr14:55495200-55517600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr14:55495200-55517600	Weak transcription	Colonic Mucosa	Colon
6	chr14:55495200-55517800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
7	chr14:55495200-55517800	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr14:55495400-55517600	Weak transcription	Right Ventricle	heart
9	chr14:55495600-55517600	Weak transcription	Brain Substantia Nigra	brain
10	chr14:55495600-55517600	Weak transcription	Fetal Kidney	kidney
11	chr14:55495600-55517600	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr14:55496200-55517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr14:55496200-55517600	Weak transcription	Fetal Heart	heart
14	chr14:55496800-55512600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr14:55498400-55517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
16	chr14:55501400-55517400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr14:55505600-55513000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
18	chr14:55506400-55517000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
19	chr14:55507800-55517600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
20	chr14:55508000-55516400	Weak transcription	Fetal Stomach	stomach
21	chr14:55508200-55513600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr14:55508400-55517600	Weak transcription	Fetal Intestine Small	intestine
23	chr14:55508800-55512400	Strong transcription	Monocytes-CD14+_RO01746	blood
24	chr14:55509200-55512800	Strong transcription	Primary monocytes fromperipheralblood	blood
25	chr14:55509200-55513000	Strong transcription	HSMM	muscle
26	chr14:55509400-55512600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
27	chr14:55509400-55513000	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:55509600-55512400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
29	chr14:55509600-55512400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr14:55509600-55512800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
31	chr14:55510200-55512400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
32	chr14:55510200-55517600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
33	chr14:55510200-55517800	Weak transcription	Aorta	Aorta
34	chr14:55510600-55517600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr14:55510600-55517600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
36	chr14:55510800-55516400	Weak transcription	K562	blood
37	chr14:55510800-55517400	Weak transcription	Fetal Lung	lung
38	chr14:55510800-55517600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
39	chr14:55510800-55517600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr14:55510800-55517600	Weak transcription	Colon Smooth Muscle	Colon
41	chr14:55510800-55517600	Weak transcription	Left Ventricle	heart
42	chr14:55510800-55517600	Weak transcription	Stomach Mucosa	stomach
43	chr14:55510800-55517600	Weak transcription	Spleen	Spleen
44	chr14:55510800-55517600	Weak transcription	Hela-S3	cervix
45	chr14:55510800-55517800	Weak transcription	Thymus	Thymus
46	chr14:55511000-55516600	Weak transcription	NHEK	skin
47	chr14:55511000-55516800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr14:55511000-55517000	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr14:55511000-55517200	Weak transcription	Brain Germinal Matrix	brain
50	chr14:55511000-55517200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland

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