Variant report

Variant	rs10842654
Chromosome Location	chr12:26171593-26171594
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs10505987	1.00[YRI][hapmap];0.86[AFR][1000 genomes]
rs10505989	0.88[CEU][hapmap]
rs10771254	0.88[CHB][hapmap];0.87[JPT][hapmap]
rs10842652	0.91[ASN][1000 genomes]
rs11494759	0.88[CHB][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs12304002	1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs12317401	0.90[AFR][1000 genomes]
rs12426668	1.00[CEU][hapmap]
rs1355707	0.88[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs16929780	0.87[CEU][hapmap]
rs16929815	0.87[CEU][hapmap]
rs16929857	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16929860	1.00[CEU][hapmap]
rs16929894	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs16929895	1.00[CEU][hapmap];0.85[AMR][1000 genomes]
rs16929904	0.82[CEU][hapmap];0.84[JPT][hapmap];0.85[AMR][1000 genomes]
rs16929970	0.88[CEU][hapmap]
rs16929998	1.00[CEU][hapmap];0.93[MEX][hapmap]
rs1797943	0.88[CHB][hapmap];0.89[CHD][hapmap];0.83[GIH][hapmap];0.87[JPT][hapmap];0.85[ASN][1000 genomes]
rs2343200	0.87[CEU][hapmap]
rs2643934	0.90[ASN][1000 genomes]
rs2669560	0.88[CHB][hapmap];1.00[CHD][hapmap];0.93[JPT][hapmap]
rs2669565	0.80[MEX][hapmap]
rs2669566	0.80[MEX][hapmap]
rs2729626	0.86[MEX][hapmap]
rs2729633	0.88[CHB][hapmap];0.97[CHD][hapmap];0.93[JPT][hapmap];0.92[ASN][1000 genomes]
rs2729653	0.93[ASN][1000 genomes]
rs2729654	0.90[ASN][1000 genomes]
rs3803008	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4963643	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4963644	0.87[CEU][hapmap]
rs4963947	0.87[CEU][hapmap];0.85[MEX][hapmap]
rs4963952	0.80[MEX][hapmap]
rs73079010	0.85[AMR][1000 genomes]
rs73079021	0.86[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73079023	0.83[AMR][1000 genomes]
rs73079024	0.83[AMR][1000 genomes]
rs924049	0.93[ASN][1000 genomes]
rs924052	0.86[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs949849	0.87[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs9804876	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.85[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv898931	chr12:26123345-26192936	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Active TSS Genic enhancers Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10842654	LRMP	cis	parietal	SCAN
rs10842654	ST8SIA1	cis	cerebellum	SCAN

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:26160600-26171600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:26164600-26171600	Weak transcription	NH-A	brain
3	chr12:26164800-26173200	Weak transcription	HMEC	breast
4	chr12:26165000-26171600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
5	chr12:26167200-26174200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr12:26167400-26171600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
7	chr12:26167400-26180600	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:26168800-26172600	Enhancers	NHDF-Ad	bronchial
9	chr12:26169000-26171800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
10	chr12:26169200-26172600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:26169400-26185400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr12:26169600-26173000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr12:26169600-26182000	Weak transcription	NHLF	lung
14	chr12:26170000-26173200	Enhancers	Osteobl	bone
15	chr12:26170400-26172000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr12:26170400-26172400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
17	chr12:26170600-26171600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr12:26170600-26174200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr12:26170800-26171800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr12:26170800-26171800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
21	chr12:26170800-26171800	Weak transcription	Placenta	Placenta
22	chr12:26170800-26171800	Weak transcription	Psoas Muscle	Psoas
23	chr12:26170800-26172200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr12:26170800-26173000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr12:26170800-26174000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr12:26170800-26174200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr12:26170800-26174200	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr12:26170800-26174200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
29	chr12:26170800-26174200	Weak transcription	Brain Angular Gyrus	brain
30	chr12:26170800-26174400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
31	chr12:26170800-26174400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr12:26170800-26174400	Weak transcription	Brain Hippocampus Middle	brain
33	chr12:26170800-26174400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
34	chr12:26170800-26174400	Weak transcription	Fetal Heart	heart
35	chr12:26170800-26174400	Weak transcription	Fetal Intestine Small	intestine
36	chr12:26170800-26174400	Weak transcription	Left Ventricle	heart
37	chr12:26170800-26174400	Weak transcription	Lung	lung
38	chr12:26170800-26174400	Weak transcription	Ovary	ovary
39	chr12:26170800-26174400	Weak transcription	Right Atrium	heart
40	chr12:26170800-26174400	Weak transcription	Right Ventricle	heart
41	chr12:26170800-26174600	Weak transcription	Brain Cingulate Gyrus	brain
42	chr12:26170800-26174800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr12:26170800-26175000	Weak transcription	Skeletal Muscle Female	skeletal muscle
44	chr12:26170800-26181600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
45	chr12:26170800-26182000	Weak transcription	Pancreas	Pancrea
46	chr12:26170800-26185600	Weak transcription	Aorta	Aorta
47	chr12:26171000-26173200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
48	chr12:26171000-26174200	Weak transcription	H1 Cell Line	embryonic stem cell
49	chr12:26171000-26174200	Weak transcription	HUES48 Cell Line	embryonic stem cell
50	chr12:26171000-26174200	Weak transcription	HUES6 Cell Line	embryonic stem cell

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