Variant report

Variant	rs4886554
Chromosome Location	chr15:78344922-78344923
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78344342-78345090	l_1195_chr15:78344341-78421177_testes
2	lnc-TBC1D2B-4	chr15:78342467-78345090	ucscGeneNc_uc002bfo_2

Extended variants
information (count: 51 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:49)

rs_ID	r²[population]
rs1004855	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[JPT][hapmap];0.83[EUR][1000 genomes]
rs10519181	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs11072716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634607	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[MEX][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638311	0.83[ASN][1000 genomes]
rs11852768	0.99[ASN][1000 genomes]
rs12148365	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.80[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12442213	0.83[CHB][hapmap];0.81[JPT][hapmap]
rs12591418	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[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594823	1.00[ASW][hapmap];0.91[CHB][hapmap];0.97[CHD][hapmap];0.93[GIH][hapmap];0.82[JPT][hapmap];0.93[LWK][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes]
rs12899061	0.81[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.98[ASN][1000 genomes]
rs12907701	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907814	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911332	1.00[CEU][hapmap];0.95[CHB][hapmap];0.84[JPT][hapmap];0.81[EUR][1000 genomes]
rs12916362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs1348257	0.92[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs17477813	0.82[ASW][hapmap];0.92[CEU][hapmap];0.81[GIH][hapmap];0.90[MEX][hapmap];0.81[AMR][1000 genomes]
rs1837913	1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap];0.81[JPT][hapmap];0.89[YRI][hapmap]
rs2028546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2044099	1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.82[MEX][hapmap]
rs2867985	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2903702	0.98[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.97[CHD][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap];0.95[CHD][hapmap]
rs4886553	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886555	0.96[ASN][1000 genomes]
rs4886994	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4886995	0.83[CHB][hapmap];0.82[JPT][hapmap]
rs4886996	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886999	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[TSI][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs56317829	0.93[ASN][1000 genomes]
rs57220134	0.97[ASN][1000 genomes]
rs58578288	0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62011511	0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7166819	0.99[ASN][1000 genomes]
rs7170746	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173128	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];0.87[TSI][hapmap];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.95[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap]
rs7181594	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029562	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030873	0.86[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs8030999	0.94[ASW][hapmap];0.84[LWK][hapmap];0.86[YRI][hapmap]
rs9047	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv529491	chr15:77932659-78751516	Genic enhancers Bivalent Enhancer Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	80 gene(s)	inside rSNPs	diseases
2	nsv1051558	chr15:78315542-78364947	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4886554	ISL2	cis	parietal	SCAN
rs4886554	CLK3	cis	cerebellum	SCAN
rs4886554	HEXA	cis	parietal	SCAN

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78296200-78358200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr15:78309200-78354200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr15:78331400-78348600	Weak transcription	A549	lung
5	chr15:78331600-78348600	Weak transcription	K562	blood
6	chr15:78337000-78347800	Weak transcription	Ovary	ovary
7	chr15:78338600-78345400	Enhancers	Duodenum Mucosa	Duodenum
8	chr15:78338800-78347000	Genic enhancers	Fetal Thymus	thymus
9	chr15:78339000-78345000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:78339000-78345000	Enhancers	Small Intestine	intestine
11	chr15:78339000-78345200	Genic enhancers	Fetal Stomach	stomach
12	chr15:78339000-78345400	Enhancers	Primary B cells from cord blood	blood
13	chr15:78339000-78346400	Enhancers	Skeletal Muscle Female	skeletal muscle
14	chr15:78340000-78345200	Enhancers	Right Atrium	heart
15	chr15:78340000-78345200	Enhancers	NH-A	brain
16	chr15:78340800-78346200	Genic enhancers	Liver	Liver
17	chr15:78341200-78345200	Genic enhancers	Fetal Lung	lung
18	chr15:78341400-78345600	Enhancers	Brain Cingulate Gyrus	brain
19	chr15:78341800-78345600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:78342000-78345000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
21	chr15:78342000-78345000	Enhancers	Colonic Mucosa	Colon
22	chr15:78342000-78345200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
23	chr15:78342200-78345000	Enhancers	Fetal Intestine Large	intestine
24	chr15:78342200-78345600	Enhancers	Primary neutrophils fromperipheralblood	blood
25	chr15:78342400-78345000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr15:78342400-78345400	Weak transcription	Aorta	Aorta
27	chr15:78342400-78345400	Enhancers	Brain Anterior Caudate	brain
28	chr15:78342400-78345600	Enhancers	Fetal Heart	heart
29	chr15:78342600-78345000	Weak transcription	Brain Germinal Matrix	brain
30	chr15:78342600-78345200	Genic enhancers	HSMM	muscle
31	chr15:78342600-78345400	Enhancers	Primary hematopoietic stem cells	blood
32	chr15:78342600-78345400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
33	chr15:78342600-78345400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
34	chr15:78342600-78348600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr15:78342800-78345200	Enhancers	Muscle Satellite Cultured Cells	--
36	chr15:78342800-78345200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr15:78342800-78345400	Enhancers	Stomach Mucosa	stomach
38	chr15:78342800-78345800	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
39	chr15:78342800-78348600	Enhancers	Primary T helper naive cells from peripheral blood	blood
40	chr15:78343000-78345000	Genic enhancers	Monocytes-CD14+_RO01746	blood
41	chr15:78343000-78348400	Weak transcription	HMEC	breast
42	chr15:78343200-78346400	Genic enhancers	Fetal Muscle Leg	muscle
43	chr15:78343200-78354200	Weak transcription	HUES48 Cell Line	embryonic stem cell
44	chr15:78343400-78345200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:78343400-78348600	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:78343600-78345400	Weak transcription	Placenta Amnion	Placenta Amnion
47	chr15:78343600-78345400	Genic enhancers	NHDF-Ad	bronchial
48	chr15:78343600-78345800	Enhancers	Adipose Nuclei	Adipose
49	chr15:78343600-78348400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:78343600-78348600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links