Variant report

Variant	rs4886996
Chromosome Location	chr15:78344268-78344269
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TBC1D2B-4	chr15:78342467-78345090	ucscGeneNc_uc002bfo_2

Extended variants
information (count: 50 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs1004855	0.89[CEU][hapmap];0.91[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.82[EUR][1000 genomes]
rs10519181	0.95[CHB][hapmap]
rs11072716	0.91[CHB][hapmap];0.91[JPT][hapmap]
rs11631578	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634607	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11638311	0.83[ASN][1000 genomes]
rs11852768	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12148365	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs12442213	0.84[CHB][hapmap];0.82[JPT][hapmap]
rs12591418	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12594823	0.91[CHB][hapmap];0.82[JPT][hapmap]
rs12899061	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12901812	0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs12907701	0.82[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12907814	0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12911332	0.87[CEU][hapmap];0.95[CHB][hapmap];0.85[JPT][hapmap];0.80[EUR][1000 genomes]
rs12916362	0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1348257	0.82[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.98[ASN][1000 genomes]
rs1442293	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1837913	1.00[CHB][hapmap];0.91[JPT][hapmap];0.97[ASN][1000 genomes]
rs1992470	0.91[CHB][hapmap];0.83[JPT][hapmap]
rs2028546	0.91[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2044099	1.00[CHB][hapmap];0.82[JPT][hapmap];0.82[ASN][1000 genomes]
rs2241885	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs2867985	0.81[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.96[ASN][1000 genomes]
rs2903702	0.94[AFR][1000 genomes];0.84[AMR][1000 genomes];0.98[ASN][1000 genomes]
rs3803380	1.00[CHB][hapmap];0.82[JPT][hapmap];0.93[ASN][1000 genomes]
rs4395040	0.95[CHB][hapmap]
rs4886553	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4886554	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[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]
rs4886999	0.88[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4887000	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs56317829	0.93[ASN][1000 genomes]
rs57220134	0.97[ASN][1000 genomes]
rs58578288	0.98[ASN][1000 genomes]
rs62011511	0.98[ASN][1000 genomes]
rs7166819	0.93[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7170746	0.89[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173128	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7174489	0.86[CHB][hapmap];0.91[JPT][hapmap]
rs7181594	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8029562	0.82[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8030873	0.87[CHB][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs9047	0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 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
3	esv3384003	chr15:78344218-78344443	Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription	lncRNA	n/a	inside rSNPs	n/a

No data

Chromatin state (count:126 , 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	chr15:78317000-78344400	Weak transcription	H1 Cell Line	embryonic stem cell
4	chr15:78317800-78344400	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:78317800-78344400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr15:78327600-78351400	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr15:78331200-78344400	Weak transcription	Psoas Muscle	Psoas
8	chr15:78331400-78348600	Weak transcription	A549	lung
9	chr15:78331600-78348600	Weak transcription	K562	blood
10	chr15:78336600-78344400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
11	chr15:78337000-78347800	Weak transcription	Ovary	ovary
12	chr15:78337200-78344400	Enhancers	Primary T helper cells fromperipheralblood	blood
13	chr15:78337800-78344600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:78338200-78344400	Enhancers	Rectal Mucosa Donor 31	rectum
15	chr15:78338600-78345400	Enhancers	Duodenum Mucosa	Duodenum
16	chr15:78338800-78344600	Enhancers	Primary monocytes fromperipheralblood	blood
17	chr15:78338800-78344800	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr15:78338800-78347000	Genic enhancers	Fetal Thymus	thymus
19	chr15:78339000-78344800	Enhancers	Colon Smooth Muscle	Colon
20	chr15:78339000-78345000	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
21	chr15:78339000-78345000	Enhancers	Small Intestine	intestine
22	chr15:78339000-78345200	Genic enhancers	Fetal Stomach	stomach
23	chr15:78339000-78345400	Enhancers	Primary B cells from cord blood	blood
24	chr15:78339000-78346400	Enhancers	Skeletal Muscle Female	skeletal muscle
25	chr15:78339200-78344800	Enhancers	Brain Angular Gyrus	brain
26	chr15:78339200-78344800	Enhancers	Duodenum Smooth Muscle	Duodenum
27	chr15:78339400-78344600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr15:78340000-78345200	Enhancers	Right Atrium	heart
29	chr15:78340000-78345200	Enhancers	NH-A	brain
30	chr15:78340200-78344800	Enhancers	Brain Hippocampus Middle	brain
31	chr15:78340600-78344400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
32	chr15:78340800-78344400	Weak transcription	Gastric	stomach
33	chr15:78340800-78346200	Genic enhancers	Liver	Liver
34	chr15:78341200-78345200	Genic enhancers	Fetal Lung	lung
35	chr15:78341400-78344400	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
36	chr15:78341400-78344800	Weak transcription	Esophagus	oesophagus
37	chr15:78341400-78344800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
38	chr15:78341400-78345600	Enhancers	Brain Cingulate Gyrus	brain
39	chr15:78341800-78344800	Enhancers	Fetal Brain Female	brain
40	chr15:78341800-78345600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
41	chr15:78342000-78344400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:78342000-78344600	Enhancers	Primary B cells from peripheral blood	blood
43	chr15:78342000-78345000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:78342000-78345000	Enhancers	Colonic Mucosa	Colon
45	chr15:78342000-78345200	Genic enhancers	Sigmoid Colon	Sigmoid Colon
46	chr15:78342200-78345000	Enhancers	Fetal Intestine Large	intestine
47	chr15:78342200-78345600	Enhancers	Primary neutrophils fromperipheralblood	blood
48	chr15:78342400-78344600	Enhancers	Primary T cells fromperipheralblood	blood
49	chr15:78342400-78344600	Enhancers	Dnd41	blood
50	chr15:78342400-78344800	Enhancers	Thymus	Thymus

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