Variant report

Variant	rs12864882
Chromosome Location	chr13:49198457-49198458
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 66 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs1009719	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12050047	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12583212	0.94[ASN][1000 genomes]
rs12583622	0.94[ASN][1000 genomes]
rs12585234	0.94[ASN][1000 genomes]
rs12855185	0.85[EUR][1000 genomes]
rs12859099	0.87[EUR][1000 genomes]
rs12867110	0.94[ASN][1000 genomes]
rs12867640	0.94[ASN][1000 genomes]
rs12870838	0.91[ASN][1000 genomes]
rs12870872	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12871411	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12871822	0.92[ASN][1000 genomes]
rs12876715	0.92[ASN][1000 genomes]
rs12876717	0.82[EUR][1000 genomes]
rs12877288	0.84[EUR][1000 genomes]
rs1326697	0.98[ASN][1000 genomes]
rs1359107	0.84[ASN][1000 genomes]
rs1476406	0.92[ASN][1000 genomes]
rs1808060	0.83[EUR][1000 genomes]
rs1980838	0.90[ASN][1000 genomes]
rs1980839	0.90[ASN][1000 genomes]
rs198563	0.80[CEU][hapmap]
rs198584	0.80[CEU][hapmap]
rs198590	0.80[CEU][hapmap]
rs2146861	0.90[ASN][1000 genomes]
rs2148516	0.98[ASN][1000 genomes]
rs34119347	0.94[ASN][1000 genomes]
rs36088391	0.94[ASN][1000 genomes]
rs59136233	0.98[ASN][1000 genomes]
rs59927903	0.92[ASN][1000 genomes]
rs7331325	0.94[ASN][1000 genomes]
rs7987608	0.87[ASN][1000 genomes]
rs7988330	0.94[ASN][1000 genomes]
rs7989251	0.87[ASN][1000 genomes]
rs9316381	0.80[CEU][hapmap]
rs9316388	0.80[CEU][hapmap]
rs9316407	0.85[EUR][1000 genomes]
rs9535049	0.84[EUR][1000 genomes]
rs9535055	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535056	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9535058	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9535061	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9562835	0.82[ASN][1000 genomes]
rs9562836	0.82[ASN][1000 genomes]
rs9568057	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568060	0.99[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568063	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9568066	0.92[ASN][1000 genomes]
rs9568067	0.98[ASN][1000 genomes]
rs9568068	0.98[ASN][1000 genomes]
rs9568070	0.92[ASN][1000 genomes]
rs9568071	0.98[ASN][1000 genomes]
rs9568072	0.92[ASN][1000 genomes]
rs9568075	0.94[ASN][1000 genomes]
rs9568077	0.82[ASN][1000 genomes]
rs9634815	0.94[ASN][1000 genomes]
rs9634816	0.94[ASN][1000 genomes]
rs9634817	0.94[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1041275	chr13:49045566-49242357	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer 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	14 gene(s)	inside rSNPs	diseases
2	nsv541769	chr13:49045566-49242357	Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Genic enhancers Active TSS Strong transcription ZNF genes & repeats 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	14 gene(s)	inside rSNPs	diseases
3	nsv832604	chr13:49061081-49281807	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv1049117	chr13:49089476-49928945	Enhancers Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
5	nsv832605	chr13:49171305-49344970	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
6	esv3495983	chr13:49181790-49222165	Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Bivalent Enhancer Genic enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
7	esv3495984	chr13:49181790-49222165	Enhancers Flanking Active TSS ZNF genes & repeats Weak transcription Genic enhancers Bivalent Enhancer	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12864882	LPAR6	cis	parietal	SCAN
rs12864882	C13orf1	cis	cerebellum	SCAN
rs12864882	ATAD2	trans	parietal	SCAN
rs12864882	ITM2B	cis	lymphoblastoid	seeQTL
rs12864882	ITM2B	Cis_1M	lymphoblastoid	RTeQTL
rs12864882	CYSLTR2	cis	lymphoblastoid	seeQTL

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:49196400-49199800	Weak transcription	Stomach Mucosa	stomach
2	chr13:49196600-49201800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr13:49196800-49205600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
4	chr13:49197000-49198600	Weak transcription	Monocytes-CD14+_RO01746	blood
5	chr13:49197400-49202000	Enhancers	Ovary	ovary
6	chr13:49197600-49202200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
7	chr13:49197800-49199800	Enhancers	Brain Hippocampus Middle	brain
8	chr13:49197800-49200400	Enhancers	Dnd41	blood
9	chr13:49197800-49202000	Enhancers	Placenta	Placenta
10	chr13:49198000-49199000	Enhancers	Brain Angular Gyrus	brain
11	chr13:49198000-49199200	Enhancers	Brain Substantia Nigra	brain
12	chr13:49198000-49205000	Enhancers	Fetal Intestine Large	intestine
13	chr13:49198200-49199400	Weak transcription	Primary hematopoietic stem cells	blood
14	chr13:49198200-49199400	Weak transcription	Pancreas	Pancrea
15	chr13:49198200-49199800	Enhancers	Brain Cingulate Gyrus	brain
16	chr13:49198400-49199400	Weak transcription	K562	blood
17	chr13:49198400-49200000	Enhancers	Brain Anterior Caudate	brain
18	chr13:49198400-49201200	Enhancers	Primary monocytes fromperipheralblood	blood

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