Variant report

Variant	rs17128132
Chromosome Location	chr14:55506757-55506758
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:55492686..55497311-chr14:55504038..55508134,4	MCF-7	breast:
2	chr14:55500498..55502436-chr14:55505187..55507055,2	K562	blood:
3	chr14:55496907..55498927-chr14:55505184..55506760,2	MCF-7	breast:
4	chr14:55506406..55509029-chr2:157190580..157192206,2	MCF-7	breast:
5	chr14:55500498..55503547-chr14:55504046..55507055,3	K562	blood:

Variant related genes	Relation type
ENSG00000198554	Chromatin interaction
ENSG00000180008	Chromatin interaction

Extended variants
information (count: 54 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:53)

rs_ID	r²[population]
rs1002054	1.00[CHB][hapmap];0.87[JPT][hapmap];0.90[ASN][1000 genomes]
rs10135721	0.89[ASN][1000 genomes]
rs10145170	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10145268	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs10220693	0.87[ASN][1000 genomes]
rs11622128	0.85[JPT][hapmap]
rs11625204	0.86[JPT][hapmap]
rs11626816	0.86[JPT][hapmap]
rs11627884	0.86[JPT][hapmap]
rs11849090	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11849878	0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11851178	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1187873	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs1187874	0.86[JPT][hapmap];0.83[ASN][1000 genomes]
rs1187876	1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187877	0.89[ASW][hapmap];1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1187878	0.84[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.86[MKK][hapmap];1.00[TSI][hapmap];0.86[YRI][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1187881	0.84[ASN][1000 genomes]
rs1187882	0.81[CEU][hapmap];0.86[CHB][hapmap];0.93[JPT][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1201378	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1209087	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1212641	0.86[JPT][hapmap];0.85[ASN][1000 genomes]
rs13379159	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs17128128	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17128145	0.89[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.87[GIH][hapmap];0.93[JPT][hapmap];0.83[LWK][hapmap];0.86[MKK][hapmap];0.92[TSI][hapmap];0.90[YRI][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17832311	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs1952085	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]
rs2147963	0.86[JPT][hapmap]
rs2251366	1.00[CHB][hapmap];0.87[JPT][hapmap];0.80[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];0.97[TSI][hapmap];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs55843949	0.82[ASN][1000 genomes]
rs56725788	0.90[ASN][1000 genomes]
rs60805089	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6572999	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs6573000	0.88[ASN][1000 genomes]
rs7141975	0.88[ASN][1000 genomes]
rs7144652	1.00[CHB][hapmap];0.88[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.87[ASN][1000 genomes]
rs7149965	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7150145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7151224	0.89[ASN][1000 genomes]
rs7151431	0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7161656	0.89[ASN][1000 genomes]
rs748017	0.82[ASN][1000 genomes]
rs8005399	1.00[CHB][hapmap];0.92[CHD][hapmap];0.87[JPT][hapmap];0.83[TSI][hapmap];0.90[ASN][1000 genomes]
rs8008134	1.00[CHB][hapmap];0.92[CHD][hapmap];0.93[JPT][hapmap];0.83[TSI][hapmap];0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8012156	0.93[CHB][hapmap];0.87[JPT][hapmap]
rs8021929	0.86[ASN][1000 genomes]
rs8022238	0.85[ASN][1000 genomes]
rs8022405	0.81[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9323278	0.90[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
rs17128132	ATG14	cis	parietal	SCAN
rs17128132	RPL13AP3	cis	cerebellum	SCAN
rs17128132	WDHD1	cis	parietal	SCAN
rs17128132	FBXO34	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:55494400-55509800	Weak transcription	Spleen	Spleen
2	chr14:55494400-55517600	Weak transcription	Lung	lung
3	chr14:55494600-55509800	Weak transcription	Gastric	stomach
4	chr14:55495000-55509800	Weak transcription	Ovary	ovary
5	chr14:55495000-55517600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr14:55495000-55517600	Weak transcription	Esophagus	oesophagus
7	chr14:55495200-55507600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr14:55495200-55509800	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr14:55495200-55510400	Weak transcription	Psoas Muscle	Psoas
10	chr14:55495200-55517600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
11	chr14:55495200-55517600	Weak transcription	Colonic Mucosa	Colon
12	chr14:55495200-55517800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
13	chr14:55495200-55517800	Weak transcription	Placenta Amnion	Placenta Amnion
14	chr14:55495400-55509800	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr14:55495400-55517600	Weak transcription	Right Ventricle	heart
16	chr14:55495600-55509800	Weak transcription	Aorta	Aorta
17	chr14:55495600-55509800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr14:55495600-55509800	Weak transcription	Rectal Smooth Muscle	rectum
19	chr14:55495600-55510000	Weak transcription	Colon Smooth Muscle	Colon
20	chr14:55495600-55510000	Weak transcription	Fetal Brain Female	brain
21	chr14:55495600-55517600	Weak transcription	Brain Substantia Nigra	brain
22	chr14:55495600-55517600	Weak transcription	Fetal Kidney	kidney
23	chr14:55495600-55517600	Weak transcription	Skeletal Muscle Male	skeletal muscle
24	chr14:55496000-55509800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
25	chr14:55496000-55510400	Weak transcription	Brain Cingulate Gyrus	brain
26	chr14:55496200-55509800	Weak transcription	Brain Inferior Temporal Lobe	brain
27	chr14:55496200-55509800	Weak transcription	Skeletal Muscle Female	skeletal muscle
28	chr14:55496200-55509800	Weak transcription	NHLF	lung
29	chr14:55496200-55510000	Weak transcription	Brain Anterior Caudate	brain
30	chr14:55496200-55510400	Weak transcription	Brain Germinal Matrix	brain
31	chr14:55496200-55510400	Weak transcription	Fetal Lung	lung
32	chr14:55496200-55517600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr14:55496200-55517600	Weak transcription	Fetal Heart	heart
34	chr14:55496400-55510000	Weak transcription	Liver	Liver
35	chr14:55496400-55510000	Weak transcription	Fetal Brain Male	brain
36	chr14:55496800-55509600	Weak transcription	Thymus	Thymus
37	chr14:55496800-55510000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
38	chr14:55496800-55510000	Weak transcription	Brain Angular Gyrus	brain
39	chr14:55496800-55510200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
40	chr14:55496800-55512600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
41	chr14:55498400-55507200	Strong transcription	Monocytes-CD14+_RO01746	blood
42	chr14:55498400-55509800	Weak transcription	K562	blood
43	chr14:55498400-55517600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr14:55498600-55507000	Strong transcription	Primary T cells fromperipheralblood	blood
45	chr14:55498600-55509800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
46	chr14:55498600-55510000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
47	chr14:55498600-55510000	Weak transcription	NH-A	brain
48	chr14:55500600-55507000	Strong transcription	Fetal Thymus	thymus
49	chr14:55500600-55507400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
50	chr14:55501400-55517400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links