Variant report

Variant	rs12817578
Chromosome Location	chr12:29500012-29500013
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:0)
Chromatin interactive
region (count:5)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CEBPB	chr12:29499723-29500052	HepG2	liver:	n/a	n/a

No data

(count:5 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr12:29499280..29501346-chr12:29531845..29534731,2	K562	blood:
2	chr12:29499488..29501163-chr12:29507438..29509843,2	K562	blood:
3	chr12:29499532..29501346-chr12:29533178..29534731,2	K562	blood:
4	chr12:29498293..29500555-chr12:29501942..29504779,3	K562	blood:
5	chr12:29498533..29501575-chr12:29526355..29528715,3	K562	blood:

No data

Variant related genes	Relation type
ERGIC2	TF binding region
ENSG00000087502	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs10492383	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11608616	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11609540	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11610197	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611420	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11611687	0.85[EUR][1000 genomes]
rs11612172	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11613628	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11615636	0.85[EUR][1000 genomes]
rs12809493	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12810064	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12810315	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12811201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12811723	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813520	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813731	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12813789	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12813996	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12814180	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12814930	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12815222	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12816511	0.84[EUR][1000 genomes]
rs12817163	0.84[EUR][1000 genomes]
rs12817825	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12817985	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12819896	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821498	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12821559	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12821708	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823372	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12823422	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12823485	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12823903	0.85[EUR][1000 genomes]
rs12824407	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12829666	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12830274	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12830493	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12830678	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12830906	0.85[EUR][1000 genomes]
rs12831730	0.97[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12832038	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12832263	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1988943	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2350312	0.85[EUR][1000 genomes]
rs2882377	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35618989	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs35636563	0.85[EUR][1000 genomes]
rs36126531	0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs3764952	0.83[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67280216	0.85[EUR][1000 genomes]
rs7134744	0.90[AMR][1000 genomes];0.88[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7295387	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7308372	0.90[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7314594	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7961336	0.85[EUR][1000 genomes]
rs7964254	0.85[EUR][1000 genomes]
rs7979654	0.80[AMR][1000 genomes];0.84[EUR][1000 genomes];0.91[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	nsv995123	chr12:29095272-29571558	Weak transcription Flanking Active TSS Enhancers Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
2	nsv1053641	chr12:29268813-29854413	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs12817578	RP11-996F15.2	cis	Thyroid	GTEx
rs12817578	RP11-996F15.2	cis	Skin Sun Exposed Lower leg	GTEx
rs12817578	RP11-996F15.2	cis	Esophagus Mucosa	GTEx
rs12817578	RP11-996F15.2	cis	Nerve Tibial	GTEx
rs12817578	RP11-996F15.2	cis	lung	GTEx
rs12817578	RP11-996F15.2	cis	Artery Tibial	GTEx
rs12817578	RP11-996F15.2	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:29427200-29527400	Weak transcription	Small Intestine	intestine
2	chr12:29462600-29533000	Weak transcription	Aorta	Aorta
3	chr12:29470800-29508400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr12:29470800-29532800	Weak transcription	Right Ventricle	heart
5	chr12:29473800-29522600	Weak transcription	NHEK	skin
6	chr12:29476000-29502600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
7	chr12:29476200-29509400	Weak transcription	Spleen	Spleen
8	chr12:29476200-29512800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr12:29476200-29533400	Weak transcription	Pancreas	Pancrea
10	chr12:29476400-29509600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr12:29476400-29532600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr12:29476400-29533200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
13	chr12:29477000-29517800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
14	chr12:29482200-29501400	Strong transcription	Primary neutrophils fromperipheralblood	blood
15	chr12:29483400-29518000	Weak transcription	Brain Hippocampus Middle	brain
16	chr12:29484200-29532000	Weak transcription	Fetal Brain Male	brain
17	chr12:29485600-29533400	Weak transcription	Gastric	stomach
18	chr12:29486800-29528600	Weak transcription	Psoas Muscle	Psoas
19	chr12:29487000-29533000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr12:29487800-29501400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr12:29488600-29503800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr12:29488800-29532000	Weak transcription	NHLF	lung
23	chr12:29489600-29525600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr12:29489800-29510000	Weak transcription	Brain Germinal Matrix	brain
25	chr12:29490000-29502800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr12:29490000-29533400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr12:29490000-29533400	Weak transcription	Esophagus	oesophagus
28	chr12:29490200-29502000	Strong transcription	Monocytes-CD14+_RO01746	blood
29	chr12:29490200-29502200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
30	chr12:29490200-29506000	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr12:29490400-29500600	Strong transcription	Dnd41	blood
32	chr12:29490400-29502800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr12:29490400-29524600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr12:29490600-29502000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
35	chr12:29490600-29503000	Strong transcription	Primary monocytes fromperipheralblood	blood
36	chr12:29491000-29511400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:29491200-29501000	Strong transcription	Primary T cells fromperipheralblood	blood
38	chr12:29491200-29502600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
39	chr12:29491400-29506400	Strong transcription	Primary T helper cells PMA-I stimulated	--
40	chr12:29492200-29502800	Strong transcription	Placenta	Placenta
41	chr12:29492400-29502000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
42	chr12:29492400-29511800	Strong transcription	HUES64 Cell Line	embryonic stem cell
43	chr12:29492400-29518000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
44	chr12:29492800-29500600	Strong transcription	Primary B cells from peripheral blood	blood
45	chr12:29492800-29500800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
46	chr12:29492800-29500800	Strong transcription	Primary hematopoietic stem cells	blood
47	chr12:29492800-29511800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
48	chr12:29492800-29519000	Weak transcription	HepG2	liver
49	chr12:29493000-29501000	Strong transcription	Osteobl	bone
50	chr12:29493000-29503200	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow

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