Variant report

Variant	rs28455654
Chromosome Location	chr15:58973705-58973706
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 123 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:119)

rs_ID	r²[population]
rs11071391	0.85[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11071392	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11071393	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.92[GIH][hapmap];0.95[JPT][hapmap];1.00[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11071397	0.86[GIH][hapmap]
rs12437457	0.86[CEU][hapmap];0.94[GIH][hapmap];0.87[MEX][hapmap];0.92[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12437952	0.81[AMR][1000 genomes]
rs12437955	0.86[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12437998	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12438487	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12438810	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12439231	0.93[CEU][hapmap];0.83[AMR][1000 genomes]
rs12440091	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12440246	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12440267	0.90[AMR][1000 genomes]
rs12441313	0.93[CEU][hapmap];0.90[AMR][1000 genomes]
rs12441912	0.93[CEU][hapmap];0.92[AMR][1000 genomes]
rs12442451	0.93[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12442956	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591291	0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12591310	0.86[GIH][hapmap]
rs12591543	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12592332	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.86[TSI][hapmap];0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12592750	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12594742	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12708455	1.00[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12901989	0.86[CEU][hapmap];0.85[EUR][1000 genomes]
rs12905110	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs12905173	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12906705	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12906714	0.93[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12907237	0.91[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12908165	0.93[CEU][hapmap];0.87[MKK][hapmap];0.85[TSI][hapmap];0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12908261	0.93[CEU][hapmap];0.92[AMR][1000 genomes]
rs12908449	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12912286	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12912327	0.98[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12913383	0.87[CEU][hapmap];0.95[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];0.94[MEX][hapmap];0.82[AMR][1000 genomes]
rs12915950	0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916010	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12917500	0.81[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12917577	0.86[CEU][hapmap];0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1365772	0.80[CHD][hapmap]
rs1426652	0.89[GIH][hapmap];0.81[MEX][hapmap]
rs1551445	0.86[GIH][hapmap]
rs16940587	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.81[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16940589	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs16940647	0.93[CEU][hapmap];1.00[CHB][hapmap];0.86[JPT][hapmap];0.89[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs16940651	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.81[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17236194	0.93[CEU][hapmap];0.84[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes]
rs17301905	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs17301954	0.88[AMR][1000 genomes]
rs1820548	0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2052804	0.96[AMR][1000 genomes];0.84[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2052805	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.87[MKK][hapmap];0.93[TSI][hapmap];1.00[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2303532	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2305421	0.82[ASW][hapmap];0.86[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];0.94[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28417700	0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28457680	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28470809	0.83[AMR][1000 genomes]
rs28489732	0.90[AMR][1000 genomes]
rs28536555	0.83[AMR][1000 genomes]
rs28542491	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28549001	0.83[AMR][1000 genomes]
rs28573205	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28576281	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs28584993	0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28600144	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28609304	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28637832	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28639679	0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28678478	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28722857	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs28724298	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28728383	0.83[EUR][1000 genomes]
rs28734088	0.82[EUR][1000 genomes]
rs28818840	0.92[AMR][1000 genomes]
rs28852159	0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34793995	0.88[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35499736	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35956992	0.94[AMR][1000 genomes]
rs6074	0.85[TSI][hapmap]
rs6494030	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6494031	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6494032	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6494033	0.93[CEU][hapmap];0.80[EUR][1000 genomes]
rs6494034	0.92[CEU][hapmap];0.83[AMR][1000 genomes]
rs6494038	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.81[TSI][hapmap];0.82[AMR][1000 genomes]
rs7163733	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[YRI][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7163939	0.83[AMR][1000 genomes]
rs7164620	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165035	0.93[CEU][hapmap];0.90[CHB][hapmap];0.84[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7165402	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7166076	0.93[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7166325	0.93[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];0.90[JPT][hapmap];0.92[MEX][hapmap];0.86[TSI][hapmap];0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7167528	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7169205	0.86[GIH][hapmap]
rs7170314	0.93[CEU][hapmap];0.81[EUR][1000 genomes]
rs7174175	0.85[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174386	0.82[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7174414	0.83[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178954	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7180550	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026668	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8029301	0.83[GIH][hapmap]
rs8029805	0.93[CEU][hapmap];0.97[GIH][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.82[AMR][1000 genomes]
rs8033565	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8033691	0.93[CEU][hapmap];0.82[AMR][1000 genomes]
rs8035960	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8036005	0.86[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8036448	0.86[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs8039791	1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];0.85[JPT][hapmap];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs8040358	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9302203	0.93[CEU][hapmap];0.84[CHB][hapmap];0.86[JPT][hapmap];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs9635351	0.86[CEU][hapmap];0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9744518	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9920042	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9920310	0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9920720	0.93[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9921024	0.85[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[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	nsv1051058	chr15:58519922-59092530	Strong transcription Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv542401	chr15:58519922-59092530	Strong transcription Weak transcription Active TSS Flanking Active TSS Enhancers Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
3	nsv904269	chr15:58906145-58992591	Enhancers Strong transcription ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
4	esv34110	chr15:58949991-59381634	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	87 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28455654	RNF111	cis	parietal	SCAN
rs28455654	PIGB	cis	cerebellum	SCAN

Chromatin state (count:105 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:58905000-58983200	Weak transcription	Esophagus	oesophagus
2	chr15:58905600-58976400	Weak transcription	Gastric	stomach
3	chr15:58906400-58976400	Weak transcription	Small Intestine	intestine
4	chr15:58921600-58976600	Weak transcription	Right Ventricle	heart
5	chr15:58923400-58982800	Weak transcription	Lung	lung
6	chr15:58933000-58987000	Weak transcription	Rectal Smooth Muscle	rectum
7	chr15:58934200-58976400	Weak transcription	Psoas Muscle	Psoas
8	chr15:58936000-58977000	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr15:58936200-58991400	Weak transcription	HMEC	breast
10	chr15:58947800-58976400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:58949400-58976400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:58951200-58987000	Weak transcription	NHEK	skin
13	chr15:58951600-58976400	Weak transcription	GM12878-XiMat	blood
14	chr15:58951600-58981800	Weak transcription	Fetal Brain Male	brain
15	chr15:58955200-58976400	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr15:58955200-58988400	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:58955400-58976200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
18	chr15:58956600-58974800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr15:58956600-58974800	Weak transcription	Adipose Nuclei	Adipose
20	chr15:58956600-58984400	Weak transcription	Duodenum Mucosa	Duodenum
21	chr15:58956600-58984600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
22	chr15:58956600-58987400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
23	chr15:58956800-58974200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:58956800-58980000	Weak transcription	Primary T helper cells PMA-I stimulated	--
25	chr15:58956800-58982000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
26	chr15:58957000-58976600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr15:58957400-58984400	Weak transcription	Rectal Mucosa Donor 31	rectum
28	chr15:58957600-58989200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr15:58958800-58989000	Weak transcription	Placenta Amnion	Placenta Amnion
30	chr15:58959600-58976400	Weak transcription	NH-A	brain
31	chr15:58959800-58973800	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr15:58960200-58976400	Weak transcription	HSMMtube	muscle
33	chr15:58960400-58976400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr15:58960400-58982800	Weak transcription	Aorta	Aorta
35	chr15:58960400-58989600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr15:58961400-58976400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr15:58961600-58987200	Weak transcription	Cortex derived primary cultured neurospheres	brain
38	chr15:58961800-58976400	Weak transcription	Brain Anterior Caudate	brain
39	chr15:58961800-58976400	Weak transcription	NHLF	lung
40	chr15:58961800-58976600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:58961800-58984600	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr15:58962000-58986800	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:58962000-58987200	Weak transcription	Fetal Lung	lung
44	chr15:58962200-58975800	Weak transcription	K562	blood
45	chr15:58965400-58976600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:58966400-58974200	Strong transcription	Monocytes-CD14+_RO01746	blood
47	chr15:58968200-58976400	Weak transcription	Hela-S3	cervix
48	chr15:58968200-58984000	Weak transcription	Brain Germinal Matrix	brain
49	chr15:58968400-58987000	Weak transcription	Fetal Kidney	kidney
50	chr15:58968600-58976200	Weak transcription	Liver	Liver

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links