Variant report

Variant	rs11637488
Chromosome Location	chr15:77433461-77433462
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:77432535..77435036-chr15:77437299..77439209,2	K562	blood:

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11630837	1.00[CEU][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs11631909	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11632999	0.92[JPT][hapmap]
rs11633318	0.90[ASN][1000 genomes]
rs11636803	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11638220	1.00[CEU][hapmap];0.92[JPT][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11639079	0.96[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11639197	0.96[CEU][hapmap];0.87[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];0.98[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs12904384	0.92[JPT][hapmap];0.80[TSI][hapmap]
rs12909704	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12910419	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs17382798	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs17383727	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs17383984	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs17466989	1.00[CEU][hapmap];0.90[GIH][hapmap];0.92[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17468792	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2100054	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2864082	0.91[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs34672572	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs34870981	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35598964	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4450362	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs56060493	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62008432	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs62008434	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62008455	0.90[ASN][1000 genomes]
rs6495233	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs66715204	0.89[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs71405237	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs7166293	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]
rs7176254	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7181345	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7182880	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8030500	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs8032925	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3440794	chr15:76764595-77571114	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	25 gene(s)	inside rSNPs	diseases
2	esv3367577	chr15:77015618-77442634	Genic enhancers Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases
3	nsv1040852	chr15:77160237-78137541	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
4	nsv1045376	chr15:77354671-77801487	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Active TSS Strong transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
5	nsv542443	chr15:77354671-77801487	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11637488	HMG20A	cis	parietal	SCAN
rs11637488	SGK269	cis	parietal	SCAN
rs11637488	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
2	chr15:77404600-77435600	Weak transcription	HMEC	breast
3	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
4	chr15:77412600-77435400	Weak transcription	HSMM	muscle
5	chr15:77412600-77435400	Weak transcription	NH-A	brain
6	chr15:77419600-77436400	Weak transcription	NHEK	skin
7	chr15:77419600-77449400	Weak transcription	Brain Inferior Temporal Lobe	brain
8	chr15:77419800-77436800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
9	chr15:77420400-77436600	Weak transcription	Fetal Heart	heart
10	chr15:77420400-77449800	Weak transcription	Psoas Muscle	Psoas
11	chr15:77421400-77436400	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:77423200-77435200	Weak transcription	NHLF	lung
13	chr15:77426000-77433600	Weak transcription	Esophagus	oesophagus
14	chr15:77426000-77434600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
15	chr15:77426000-77435400	Weak transcription	Spleen	Spleen
16	chr15:77426000-77435800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr15:77426000-77435800	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:77426000-77436200	Weak transcription	Fetal Muscle Leg	muscle
19	chr15:77426000-77436800	Weak transcription	Ovary	ovary
20	chr15:77426000-77437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr15:77426000-77437600	Weak transcription	Gastric	stomach
22	chr15:77426000-77449600	Weak transcription	Brain Angular Gyrus	brain
23	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
24	chr15:77426200-77435400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
25	chr15:77426200-77435600	Weak transcription	Aorta	Aorta
26	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
27	chr15:77426400-77435600	Weak transcription	HUVEC	blood vessel
28	chr15:77426400-77436400	Weak transcription	Skeletal Muscle Female	skeletal muscle
29	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
30	chr15:77428000-77449600	Weak transcription	Primary T cells from cord blood	blood
31	chr15:77429200-77434800	ZNF genes & repeats	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:77429400-77435400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
33	chr15:77429400-77435400	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr15:77430000-77435400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:77430400-77436000	Weak transcription	Stomach Mucosa	stomach
36	chr15:77431800-77434800	ZNF genes & repeats	Primary B cells from cord blood	blood
37	chr15:77432000-77434000	Weak transcription	Rectal Mucosa Donor 31	rectum
38	chr15:77432400-77435000	ZNF genes & repeats	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:77432600-77434800	ZNF genes & repeats	Liver	Liver
40	chr15:77432600-77435000	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
41	chr15:77432600-77435000	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr15:77432800-77434600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:77432800-77435000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
44	chr15:77432800-77448400	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr15:77433000-77434600	Weak transcription	NHDF-Ad	bronchial
46	chr15:77433200-77434400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
47	chr15:77433200-77435000	Weak transcription	Osteobl	bone
48	chr15:77433200-77436400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:77433200-77436600	Weak transcription	Fetal Lung	lung
50	chr15:77433200-77449200	Weak transcription	Rectal Mucosa Donor 29	rectum

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