Variant report

Variant	rs1680488
Chromosome Location	chr15:57005363-57005364
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57004343..57007295-chr15:57010153..57011779,2	K562	blood:

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1010699	0.90[EUR][1000 genomes]
rs11071282	1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs11071283	1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs11071294	0.82[TSI][hapmap]
rs11630334	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11634444	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11635201	0.91[ASN][1000 genomes]
rs11636534	0.90[EUR][1000 genomes]
rs12441674	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs1657928	0.83[EUR][1000 genomes]
rs1657932	0.83[EUR][1000 genomes]
rs1657933	0.84[EUR][1000 genomes]
rs1657942	0.83[EUR][1000 genomes]
rs1660965	0.83[EUR][1000 genomes]
rs16977060	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs16977067	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2113678	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2128172	1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs28441487	0.91[ASN][1000 genomes]
rs28463927	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs28497695	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28620046	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28678122	1.00[CHB][hapmap];0.81[CHD][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.82[ASN][1000 genomes]
rs28778716	0.83[ASN][1000 genomes]
rs28830569	0.83[ASN][1000 genomes]
rs28893316	0.83[ASN][1000 genomes]
rs4774890	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4774891	0.94[CEU][hapmap];1.00[CHB][hapmap];0.90[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs534005	0.85[ASW][hapmap];0.88[CEU][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];1.00[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.90[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7164084	0.93[CEU][hapmap];0.83[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs7182346	0.94[CEU][hapmap];1.00[CHB][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs72744954	0.83[ASN][1000 genomes]
rs72744977	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031966	0.88[CEU][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.80[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs809459	0.80[ASW][hapmap];0.94[CEU][hapmap];0.81[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.95[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[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	esv3422474	chr15:56867190-57244330	Strong transcription ZNF genes & repeats Active TSS Enhancers Weak transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:66 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:56919800-57016600	Weak transcription	Small Intestine	intestine
2	chr15:56958400-57019200	Weak transcription	Fetal Intestine Small	intestine
3	chr15:56971000-57023400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
4	chr15:56988800-57008400	Weak transcription	Fetal Heart	heart
5	chr15:56992400-57008400	Weak transcription	K562	blood
6	chr15:56992400-57010800	Weak transcription	Spleen	Spleen
7	chr15:56992400-57021800	Weak transcription	Right Ventricle	heart
8	chr15:56992600-57022600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:56993000-57016000	Weak transcription	Pancreas	Pancrea
10	chr15:56993000-57024000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:56993200-57007200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr15:56993200-57008200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
13	chr15:56993200-57010800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr15:56993200-57010800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr15:56993200-57011600	Weak transcription	HMEC	breast
16	chr15:56993400-57021600	Weak transcription	Fetal Brain Male	brain
17	chr15:56994000-57023800	Weak transcription	Fetal Kidney	kidney
18	chr15:56995800-57016000	Weak transcription	Duodenum Smooth Muscle	Duodenum
19	chr15:56995800-57022200	Weak transcription	Muscle Satellite Cultured Cells	--
20	chr15:56996000-57005400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:56996000-57008000	Weak transcription	Brain Angular Gyrus	brain
22	chr15:56996000-57009200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
23	chr15:56996000-57010800	Weak transcription	Brain Anterior Caudate	brain
24	chr15:56996000-57011000	Weak transcription	Skeletal Muscle Female	skeletal muscle
25	chr15:56996000-57011400	Weak transcription	Aorta	Aorta
26	chr15:56996000-57013000	Weak transcription	Ovary	ovary
27	chr15:56996000-57021800	Weak transcription	Rectal Smooth Muscle	rectum
28	chr15:56996400-57007600	Weak transcription	Brain Cingulate Gyrus	brain
29	chr15:56996400-57015800	Weak transcription	Fetal Intestine Large	intestine
30	chr15:56996400-57021600	Weak transcription	HSMMtube	muscle
31	chr15:56996400-57022600	Weak transcription	NH-A	brain
32	chr15:56996600-57011000	Weak transcription	Dnd41	blood
33	chr15:56996800-57022600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
34	chr15:56997000-57016000	Weak transcription	HSMM	muscle
35	chr15:56997200-57015800	Weak transcription	Liver	Liver
36	chr15:56997200-57016400	Weak transcription	Fetal Muscle Trunk	muscle
37	chr15:56997200-57016600	Weak transcription	Left Ventricle	heart
38	chr15:56997200-57022800	Weak transcription	Gastric	stomach
39	chr15:56997200-57023800	Weak transcription	Fetal Stomach	stomach
40	chr15:56997400-57010800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr15:56997400-57012400	Weak transcription	NHLF	lung
42	chr15:56997600-57011800	Weak transcription	NHDF-Ad	bronchial
43	chr15:56998000-57016000	Weak transcription	Fetal Lung	lung
44	chr15:56998400-57007400	Weak transcription	Primary hematopoietic stem cells	blood
45	chr15:56998400-57013800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
46	chr15:56998400-57013800	Weak transcription	Cortex derived primary cultured neurospheres	brain
47	chr15:56998400-57016200	Weak transcription	Monocytes-CD14+_RO01746	blood
48	chr15:56998400-57021200	Weak transcription	Stomach Smooth Muscle	stomach
49	chr15:56998600-57015800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr15:56998800-57010400	Weak transcription	Primary T helper cells fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links