Variant report

Variant	rs10882029
Chromosome Location	chr10:93955851-93955852
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs10509643	0.86[YRI][hapmap]
rs10786036	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs10882034	0.86[CHB][hapmap];0.98[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs10882035	0.93[ASN][1000 genomes]
rs10882036	0.93[ASN][1000 genomes]
rs10882039	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10882043	0.82[ASN][1000 genomes]
rs11186840	0.87[ASN][1000 genomes]
rs11186848	0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs11186851	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.94[ASN][1000 genomes]
rs11186862	0.93[ASN][1000 genomes]
rs11186869	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11186872	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs12246924	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12267769	0.82[LWK][hapmap];0.86[YRI][hapmap]
rs1935864	0.82[MKK][hapmap]
rs2011483	0.83[ASN][1000 genomes]
rs3740302	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs56072007	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs57381242	0.93[ASN][1000 genomes]
rs59386062	0.93[ASN][1000 genomes]
rs66521023	0.94[ASN][1000 genomes]
rs66882667	0.85[ASN][1000 genomes]
rs7073372	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7080101	0.83[ASN][1000 genomes]
rs7080731	0.93[ASN][1000 genomes]
rs7098170	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[YRI][hapmap];0.84[ASN][1000 genomes]
rs730075	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7900400	0.87[ASN][1000 genomes]
rs7917088	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs932820	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs9804247	0.86[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][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	nsv975763	chr10:93822289-94105956	Enhancers Bivalent Enhancer Strong transcription Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
2	nsv1046258	chr10:93866969-94466106	Active TSS Strong transcription Weak transcription Flanking Bivalent TSS/Enh Enhancers Flanking Active TSS Genic enhancers Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10882029	CYP26A1	cis	cerebellum	SCAN
rs10882029	MARCH5	cis	multi-tissue	Pritchard

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:93926400-93976000	Weak transcription	Stomach Smooth Muscle	stomach
2	chr10:93926600-93976000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr10:93926800-93982400	Weak transcription	HSMMtube	muscle
4	chr10:93927000-93963800	Weak transcription	Brain Angular Gyrus	brain
5	chr10:93927000-93966200	Weak transcription	Ovary	ovary
6	chr10:93927000-93970800	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr10:93927200-93967600	Weak transcription	Adipose Nuclei	Adipose
8	chr10:93927200-93980400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr10:93927400-93960000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
10	chr10:93927400-93966600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
11	chr10:93927400-93970800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr10:93927400-93997800	Weak transcription	Fetal Intestine Large	intestine
13	chr10:93929200-93984800	Weak transcription	Fetal Intestine Small	intestine
14	chr10:93929400-93967800	Weak transcription	Colon Smooth Muscle	Colon
15	chr10:93930000-93958200	Weak transcription	Hela-S3	cervix
16	chr10:93934200-93976200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr10:93936600-93958000	Weak transcription	Small Intestine	intestine
18	chr10:93940200-93971200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
19	chr10:93940600-93958400	Weak transcription	Brain Cingulate Gyrus	brain
20	chr10:93940600-93970800	Weak transcription	Fetal Stomach	stomach
21	chr10:93941600-93958000	Weak transcription	Brain Anterior Caudate	brain
22	chr10:93941600-93958000	Weak transcription	Brain Inferior Temporal Lobe	brain
23	chr10:93941800-93958000	Weak transcription	Brain Hippocampus Middle	brain
24	chr10:93941800-93968000	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr10:93941800-93971200	Weak transcription	Primary B cells from peripheral blood	blood
26	chr10:93943600-93958200	Weak transcription	K562	blood
27	chr10:93945800-93963800	Weak transcription	Fetal Brain Female	brain
28	chr10:93946600-93964000	Weak transcription	Left Ventricle	heart
29	chr10:93947600-93958200	Weak transcription	Brain Substantia Nigra	brain
30	chr10:93947800-93967800	Weak transcription	GM12878-XiMat	blood
31	chr10:93949000-93961800	Weak transcription	Primary T cells from cord blood	blood
32	chr10:93949800-93958200	Weak transcription	Liver	Liver
33	chr10:93952400-93958000	Weak transcription	HepG2	liver
34	chr10:93952400-93963400	Weak transcription	Monocytes-CD14+_RO01746	blood
35	chr10:93952600-93966200	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr10:93954800-93956200	Enhancers	Fetal Heart	heart

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links