Variant report

Variant	rs11632999
Chromosome Location	chr15:77436995-77436996
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 39 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11630770	0.82[ASW][hapmap];0.80[CEU][hapmap];1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs11630837	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11630843	0.91[ASN][1000 genomes]
rs11631909	0.91[ASN][1000 genomes]
rs11634056	0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11636803	0.97[ASN][1000 genomes]
rs11637488	0.92[JPT][hapmap]
rs11638220	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs11639079	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs11639197	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs12904384	1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs12909704	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs12910419	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17382798	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs17383727	0.91[ASN][1000 genomes]
rs17383984	0.91[ASN][1000 genomes]
rs17384406	0.91[ASN][1000 genomes]
rs17466989	0.90[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs2100054	0.97[ASN][1000 genomes]
rs2864082	0.91[ASN][1000 genomes]
rs33940778	0.85[JPT][hapmap]
rs34870981	0.94[ASN][1000 genomes]
rs35598964	0.94[ASN][1000 genomes]
rs4450362	1.00[ASN][1000 genomes]
rs62008430	0.85[ASN][1000 genomes]
rs62008432	0.91[ASN][1000 genomes]
rs66715204	0.97[ASN][1000 genomes]
rs71405237	1.00[ASN][1000 genomes]
rs7166293	0.92[JPT][hapmap]
rs7176254	0.91[ASN][1000 genomes]
rs7181345	1.00[ASN][1000 genomes]
rs7182880	0.94[ASN][1000 genomes]
rs8030500	1.00[ASN][1000 genomes]
rs8032925	1.00[ASN][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
rs11632999	SGK269	cis	parietal	SCAN
rs11632999	HMG20A	cis	parietal	SCAN
rs11632999	HMG20A	cis	cerebellum	SCAN

Chromatin state (count:85 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:77401600-77449600	Weak transcription	Colonic Mucosa	Colon
2	chr15:77411800-77449400	Weak transcription	Colon Smooth Muscle	Colon
3	chr15:77419600-77449400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr15:77420400-77449800	Weak transcription	Psoas Muscle	Psoas
5	chr15:77426000-77437200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr15:77426000-77437600	Weak transcription	Gastric	stomach
7	chr15:77426000-77449600	Weak transcription	Brain Angular Gyrus	brain
8	chr15:77426000-77452400	Weak transcription	Pancreas	Pancrea
9	chr15:77426200-77453200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr15:77427600-77460600	Weak transcription	Right Ventricle	heart
11	chr15:77428000-77449600	Weak transcription	Primary T cells from cord blood	blood
12	chr15:77432800-77448400	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:77433200-77449200	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr15:77433400-77449400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:77433400-77449400	Weak transcription	Brain Hippocampus Middle	brain
16	chr15:77433400-77449600	Weak transcription	Left Ventricle	heart
17	chr15:77433600-77448400	Weak transcription	Primary neutrophils fromperipheralblood	blood
18	chr15:77434200-77460400	Weak transcription	Fetal Brain Male	brain
19	chr15:77434400-77437000	Weak transcription	HepG2	liver
20	chr15:77434800-77438000	Strong transcription	Primary B cells from cord blood	blood
21	chr15:77434800-77449200	Weak transcription	Brain Anterior Caudate	brain
22	chr15:77434800-77449200	Weak transcription	Rectal Mucosa Donor 31	rectum
23	chr15:77434800-77449400	Weak transcription	Liver	Liver
24	chr15:77435000-77438600	Enhancers	Fetal Intestine Small	intestine
25	chr15:77435000-77448400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:77435000-77448600	Weak transcription	HUES64 Cell Line	embryonic stem cell
27	chr15:77435000-77449200	Weak transcription	Duodenum Smooth Muscle	Duodenum
28	chr15:77435200-77439800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
29	chr15:77435400-77437000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
30	chr15:77435400-77437000	Enhancers	Placenta Amnion	Placenta Amnion
31	chr15:77435600-77437400	Strong transcription	Fetal Muscle Trunk	muscle
32	chr15:77435600-77437600	Enhancers	HMEC	breast
33	chr15:77435600-77437600	Enhancers	HUVEC	blood vessel
34	chr15:77435600-77438000	Enhancers	Aorta	Aorta
35	chr15:77435600-77438600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr15:77435600-77438600	Enhancers	Fetal Intestine Large	intestine
37	chr15:77435800-77438000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
38	chr15:77436000-77437000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr15:77436000-77437000	Flanking Active TSS	Muscle Satellite Cultured Cells	--
40	chr15:77436000-77437000	Flanking Active TSS	Osteobl	bone
41	chr15:77436000-77437200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr15:77436000-77437200	Flanking Active TSS	NH-A	brain
43	chr15:77436000-77438200	Enhancers	Duodenum Mucosa	Duodenum
44	chr15:77436000-77438800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
45	chr15:77436000-77439800	Enhancers	Stomach Mucosa	stomach
46	chr15:77436000-77457800	Weak transcription	Spleen	Spleen
47	chr15:77436200-77437000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr15:77436200-77437000	Enhancers	Fetal Kidney	kidney
49	chr15:77436200-77437400	Strong transcription	Primary B cells from peripheral blood	blood
50	chr15:77436200-77437600	Enhancers	Fetal Muscle Leg	muscle

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