Variant report

Variant	rs10489327
Chromosome Location	chr1:175134314-175134315
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:175133817..175136393-chr1:175137880..175140113,3	K562	blood:
2	chr1:175133817..175136820-chr1:175136859..175140006,3	K562	blood:
3	chr1:175127835..175129941-chr1:175131932..175135022,3	K562	blood:

Extended variants
information (count: 14 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10489328	0.82[MEX][hapmap]
rs1057285	0.84[CHB][hapmap];0.84[CHD][hapmap];0.85[GIH][hapmap];0.82[MEX][hapmap]
rs11809587	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139918	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12139941	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16847872	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2018318	0.82[MEX][hapmap]
rs2187958	0.91[MEX][hapmap]
rs2269655	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];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3737933	0.88[CHB][hapmap];0.83[CHD][hapmap];0.88[GIH][hapmap];0.89[JPT][hapmap];0.91[MEX][hapmap];0.80[ASN][1000 genomes]
rs60259517	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73032679	0.89[AFR][1000 genomes]

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	nsv522101	chr1:175109517-175151183	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
2	nsv429924	chr1:175110480-175134314	Enhancers Bivalent/Poised TSS Strong transcription Weak transcription Bivalent Enhancer Genic enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs10489327	CACYBP	cis	parietal	SCAN
rs10489327	MRPS14	cis	cerebellum	SCAN
rs10489327	C1orf112	cis	parietal	SCAN
rs10489327	KIAA0040	cis	multi-tissue	Pritchard

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:175120000-175139400	Weak transcription	Colon Smooth Muscle	Colon
2	chr1:175122200-175136600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
3	chr1:175124000-175140400	Weak transcription	Fetal Heart	heart
4	chr1:175124400-175138200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr1:175124600-175134600	Weak transcription	Small Intestine	intestine
6	chr1:175126800-175138200	Weak transcription	Pancreatic Islets	Pancreatic Islet
7	chr1:175126800-175141800	Strong transcription	Primary B cells from cord blood	blood
8	chr1:175126800-175148800	Strong transcription	Primary monocytes fromperipheralblood	blood
9	chr1:175127000-175135600	Strong transcription	Duodenum Mucosa	Duodenum
10	chr1:175127000-175136200	Strong transcription	Thymus	Thymus
11	chr1:175127000-175136600	Strong transcription	Primary neutrophils fromperipheralblood	blood
12	chr1:175127000-175136600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr1:175127000-175148400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:175127200-175136200	Strong transcription	Fetal Thymus	thymus
15	chr1:175127200-175137800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:175127200-175139000	Strong transcription	Primary B cells from peripheral blood	blood
17	chr1:175127200-175139000	Strong transcription	Placenta	Placenta
18	chr1:175127200-175139200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr1:175127200-175147800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:175127400-175134400	Weak transcription	Brain Substantia Nigra	brain
21	chr1:175127400-175137000	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
22	chr1:175127400-175139200	Strong transcription	Primary T cells fromperipheralblood	blood
23	chr1:175127400-175144200	Strong transcription	Breast Myoepithelial Primary Cells	Breast
24	chr1:175127400-175149400	Strong transcription	Monocytes-CD14+_RO01746	blood
25	chr1:175127600-175136600	Weak transcription	HUES6 Cell Line	embryonic stem cell
26	chr1:175127600-175136800	Strong transcription	Sigmoid Colon	Sigmoid Colon
27	chr1:175127600-175137200	Strong transcription	Pancreas	Pancrea
28	chr1:175127600-175137600	Strong transcription	Primary T helper cells fromperipheralblood	blood
29	chr1:175127600-175137600	Strong transcription	Liver	Liver
30	chr1:175127600-175140600	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
31	chr1:175127800-175136000	Strong transcription	Lung	lung
32	chr1:175127800-175136400	Strong transcription	Skeletal Muscle Male	skeletal muscle
33	chr1:175127800-175139200	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr1:175127800-175140200	Strong transcription	Spleen	Spleen
35	chr1:175128200-175135000	Strong transcription	Aorta	Aorta
36	chr1:175128200-175137000	Strong transcription	Rectal Mucosa Donor 31	rectum
37	chr1:175128200-175138400	Strong transcription	Primary T helper cells PMA-I stimulated	--
38	chr1:175128200-175140000	Strong transcription	Primary T cells from cord blood	blood
39	chr1:175128400-175136000	Strong transcription	Ovary	ovary
40	chr1:175128400-175136000	Strong transcription	Skeletal Muscle Female	skeletal muscle
41	chr1:175128400-175138800	Strong transcription	GM12878-XiMat	blood
42	chr1:175128400-175139200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
43	chr1:175128600-175136600	Strong transcription	HMEC	breast
44	chr1:175128600-175136800	Strong transcription	Rectal Mucosa Donor 29	rectum
45	chr1:175128600-175138400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
46	chr1:175129000-175135800	Strong transcription	Fetal Intestine Large	intestine
47	chr1:175129000-175136200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr1:175129000-175138000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr1:175129000-175138000	Strong transcription	NHEK	skin
50	chr1:175129200-175159600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived

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