Variant report

Variant	rs11639044
Chromosome Location	chr15:79083814-79083815
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs11072803	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs11072804	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11072806	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11630236	1.00[CHB][hapmap];0.82[MEX][hapmap]
rs11631955	1.00[CHB][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11632102	0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11634042	0.92[CEU][hapmap];0.84[MEX][hapmap];0.86[TSI][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11634450	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11638321	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11856536	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs11856953	0.84[ASN][1000 genomes]
rs11858210	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs12050525	0.88[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs12592721	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12899147	0.96[CEU][hapmap];0.95[GIH][hapmap];0.89[MEX][hapmap];0.95[TSI][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12903203	0.96[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12907065	0.92[ASN][1000 genomes]
rs12913260	0.84[AMR][1000 genomes]
rs17487514	0.82[MKK][hapmap]
rs1809420	1.00[CHB][hapmap];0.89[MEX][hapmap];0.84[MKK][hapmap]
rs1825087	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1994016	0.85[CEU][hapmap];0.90[GIH][hapmap];0.89[MEX][hapmap];0.90[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1996371	0.82[MKK][hapmap]
rs2277545	0.96[CEU][hapmap];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2277546	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28610385	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs2904220	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs3825807	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4389112	0.84[ASN][1000 genomes]
rs4886590	0.82[AMR][1000 genomes]
rs4886592	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4887109	0.82[AMR][1000 genomes]
rs4887113	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66925868	0.84[ASN][1000 genomes]
rs7173267	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7174367	1.00[CHB][hapmap];0.84[MEX][hapmap]
rs7177699	0.96[CEU][hapmap];0.93[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs72749206	0.84[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	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv904431	chr15:79006442-79155088	Bivalent/Poised TSS Enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Weak transcription Genic enhancers Bivalent Enhancer Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
3	esv33573	chr15:79053484-79293881	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
4	nsv904432	chr15:79066932-79175813	Active TSS Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Genic enhancers Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11639044	HMG20A	cis	parietal	SCAN
rs11639044	CLK3	cis	parietal	SCAN
rs11639044	BCL2A1	cis	parietal	SCAN
rs11639044	CHRNA5	cis	parietal	SCAN
rs11639044	PSMA4	cis	parietal	SCAN

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:79058000-79090000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
2	chr15:79069200-79090200	Weak transcription	NHDF-Ad	bronchial
3	chr15:79072000-79096600	Weak transcription	Brain Substantia Nigra	brain
4	chr15:79072000-79096800	Weak transcription	Colon Smooth Muscle	Colon
5	chr15:79072800-79089800	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr15:79072800-79102400	Weak transcription	Fetal Kidney	kidney
7	chr15:79076400-79090400	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:79076400-79090400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:79076400-79090800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr15:79077200-79084800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr15:79077200-79085200	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr15:79077200-79089800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr15:79077200-79096600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr15:79077400-79089000	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr15:79077600-79084200	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:79077600-79087800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:79077800-79090600	Strong transcription	Brain Germinal Matrix	brain
18	chr15:79078000-79084000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
19	chr15:79078000-79084200	Strong transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:79078000-79089400	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr15:79078200-79093200	Strong transcription	Fetal Stomach	stomach
22	chr15:79078400-79085000	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
23	chr15:79078400-79091800	Weak transcription	Gastric	stomach
24	chr15:79078600-79084000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
25	chr15:79078600-79084000	Strong transcription	Adipose Nuclei	Adipose
26	chr15:79078600-79084600	Strong transcription	Fetal Muscle Trunk	muscle
27	chr15:79078600-79084800	Strong transcription	Fetal Muscle Leg	muscle
28	chr15:79078600-79085000	Strong transcription	HSMMtube	muscle
29	chr15:79078600-79089800	Weak transcription	HMEC	breast
30	chr15:79078600-79090600	Strong transcription	Fetal Brain Female	brain
31	chr15:79079000-79089600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr15:79079400-79091000	Weak transcription	HUVEC	blood vessel
33	chr15:79079600-79090600	Weak transcription	NH-A	brain
34	chr15:79080200-79084800	Strong transcription	HUES6 Cell Line	embryonic stem cell
35	chr15:79080400-79096200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr15:79080600-79087400	Weak transcription	HUES48 Cell Line	embryonic stem cell
37	chr15:79080600-79087400	Weak transcription	Osteobl	bone
38	chr15:79080800-79084400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
39	chr15:79080800-79089400	Weak transcription	NHLF	lung
40	chr15:79080800-79095200	Weak transcription	Fetal Intestine Large	intestine
41	chr15:79081000-79088600	Weak transcription	Placenta	Placenta
42	chr15:79081400-79084400	Weak transcription	Fetal Lung	lung
43	chr15:79081600-79084000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
44	chr15:79081800-79084200	Strong transcription	H1 Cell Line	embryonic stem cell
45	chr15:79081800-79084600	Strong transcription	Spleen	Spleen
46	chr15:79082000-79084400	Genic enhancers	Left Ventricle	heart
47	chr15:79082000-79088000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
48	chr15:79082400-79087800	Weak transcription	Lung	lung
49	chr15:79082600-79084000	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr15:79082600-79085000	Strong transcription	Right Ventricle	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links