Variant report

Variant	rs16908059
Chromosome Location	chr12:12588791-12588792
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:12588163..12590134-chr12:12591817..12594282,2	K562	blood:
2	chr12:12583518..12585650-chr12:12588474..12590636,2	K562	blood:
3	chr12:12587508..12589522-chr12:12868526..12870238,2	MCF-7	breast:
4	chr12:12588493..12590525-chr12:12592316..12593920,2	MCF-7	breast:
5	chr12:12586894..12590134-chr12:12591817..12594282,3	K562	blood:

Variant related genes	Relation type
ENSG00000111276	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:57)

rs_ID	r²[population]
rs10505765	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AFR][1000 genomes];0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10505767	0.82[EUR][1000 genomes]
rs10772566	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10772567	0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs10845542	0.87[ASN][1000 genomes]
rs10845544	0.87[ASN][1000 genomes]
rs11054894	0.80[ASN][1000 genomes]
rs11054963	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs11609375	0.82[CHD][hapmap]
rs11829916	0.87[ASN][1000 genomes]
rs1544682	0.87[ASN][1000 genomes]
rs16907990	1.00[CEU][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs16908050	0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16908062	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908072	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]
rs16908076	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16908101	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16908146	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908151	0.85[EUR][1000 genomes]
rs16908167	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16908171	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908188	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908204	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs16908209	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16908214	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs16916539	1.00[CEU][hapmap];0.82[EUR][1000 genomes]
rs17312766	0.81[EUR][1000 genomes]
rs17378260	0.81[EUR][1000 genomes]
rs2160586	0.82[CHD][hapmap];0.88[JPT][hapmap];0.87[ASN][1000 genomes]
rs2193269	0.83[ASN][1000 genomes]
rs2193270	1.00[CHB][hapmap];0.93[CHD][hapmap];0.83[ASN][1000 genomes]
rs2287204	0.85[EUR][1000 genomes]
rs2287205	0.85[EUR][1000 genomes]
rs28853875	0.83[ASN][1000 genomes]
rs3088226	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs3751262	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.87[EUR][1000 genomes]
rs3803098	1.00[CEU][hapmap];0.81[CHB][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap]
rs4633541	0.81[EUR][1000 genomes]
rs4763830	0.82[CHD][hapmap]
rs56089442	0.84[ASN][1000 genomes]
rs56701819	0.89[ASN][1000 genomes]
rs56796062	0.83[ASN][1000 genomes]
rs56915387	0.90[ASN][1000 genomes]
rs57348917	0.80[ASN][1000 genomes]
rs60253266	0.85[ASN][1000 genomes]
rs61543155	0.88[ASN][1000 genomes]
rs7132813	1.00[AFR][1000 genomes]
rs7135655	0.87[CHB][hapmap]
rs7300150	0.82[ASN][1000 genomes]
rs7309503	0.81[CHD][hapmap]
rs7309982	0.81[CHD][hapmap]
rs7313825	0.82[CHD][hapmap]
rs745632	0.82[EUR][1000 genomes]
rs7486371	1.00[CEU][hapmap];0.87[CHB][hapmap];0.83[CHD][hapmap];1.00[GIH][hapmap];0.88[TSI][hapmap];0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7963695	1.00[CEU][hapmap]
rs7967111	0.84[CHD][hapmap];0.82[ASN][1000 genomes]
rs9645752	0.83[JPT][hapmap]

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	nsv949003	chr12:11938229-12618690	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	36 gene(s)	inside rSNPs	diseases
2	esv1812889	chr12:12510842-12593406	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs16908059	KLRA1	cis	parietal	SCAN
rs16908059	LOH12CR1	cis	lymphoblastoid	seeQTL
rs16908059	GPRC5D	cis	parietal	SCAN
rs16908059	TAS2R7	cis	cerebellum	SCAN

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:12578800-12589200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:12581600-12588800	Weak transcription	Primary neutrophils fromperipheralblood	blood
3	chr12:12582000-12589200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:12582600-12592000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
5	chr12:12582600-12595000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
6	chr12:12582600-12599400	Weak transcription	HUES48 Cell Line	embryonic stem cell
7	chr12:12582800-12592600	Weak transcription	NH-A	brain
8	chr12:12582800-12596400	Weak transcription	Spleen	Spleen
9	chr12:12583000-12589400	Weak transcription	HSMM	muscle
10	chr12:12583000-12594000	Weak transcription	HSMMtube	muscle
11	chr12:12584000-12598600	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr12:12584200-12589200	Enhancers	Fetal Lung	lung
13	chr12:12584200-12590200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
14	chr12:12584200-12592200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
15	chr12:12584200-12592800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:12584200-12593200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr12:12584400-12592000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
18	chr12:12585400-12593200	Weak transcription	Small Intestine	intestine
19	chr12:12585600-12589200	Weak transcription	Duodenum Mucosa	Duodenum
20	chr12:12585600-12590200	Weak transcription	HMEC	breast
21	chr12:12585600-12592000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
22	chr12:12585600-12592000	Weak transcription	HUVEC	blood vessel
23	chr12:12585600-12595200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr12:12585800-12595400	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr12:12586000-12589200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr12:12586000-12589200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr12:12586000-12589400	Weak transcription	Muscle Satellite Cultured Cells	--
28	chr12:12586000-12593200	Weak transcription	Liver	Liver
29	chr12:12586000-12594200	Weak transcription	Hela-S3	cervix
30	chr12:12586000-12595000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:12586200-12589200	Weak transcription	HUES64 Cell Line	embryonic stem cell
32	chr12:12586200-12595000	Weak transcription	Colon Smooth Muscle	Colon
33	chr12:12586200-12595400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr12:12586400-12588800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr12:12586600-12594200	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr12:12586800-12590400	Weak transcription	Osteobl	bone
37	chr12:12586800-12594000	Weak transcription	Right Ventricle	heart
38	chr12:12587000-12588800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
39	chr12:12587000-12589400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr12:12587000-12590800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
41	chr12:12587000-12591800	Weak transcription	NHEK	skin
42	chr12:12587000-12592200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
43	chr12:12587000-12592600	Weak transcription	Stomach Mucosa	stomach
44	chr12:12587000-12593800	Weak transcription	Sigmoid Colon	Sigmoid Colon
45	chr12:12587000-12594800	Weak transcription	Aorta	Aorta
46	chr12:12587000-12594800	Weak transcription	Esophagus	oesophagus
47	chr12:12587000-12594800	Weak transcription	Placenta	Placenta
48	chr12:12587200-12593200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr12:12587200-12593800	Weak transcription	Fetal Intestine Small	intestine
50	chr12:12587200-12594000	Weak transcription	Brain Angular Gyrus	brain

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links