Variant report

Variant	rs12208781
Chromosome Location	chr6:73986348-73986349
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	6:73978150-73986643..6:74160392-74184826	K562	blood:
2	6:73978150-73986643..6:74062967-74076046	H1-hESC	embryonic stem cell:	embryo
3	6:73978150-73986643..6:74099986-74112890	H1-hESC	embryonic stem cell:	embryo
4	6:73978150-73986643..6:74078047-74099067	H1-hESC	embryonic stem cell:	embryo

Variant related genes	Relation type
ENSG00000135297	Chromatin interaction
ENSG00000207023	Chromatin interaction
ENSG00000203908	Chromatin interaction
ENSG00000224221	Chromatin interaction
ENSG00000235174	Chromatin interaction
ENSG00000203909	Chromatin interaction
ENSG00000164430	Chromatin interaction
ENSG00000080007	Chromatin interaction
ENSG00000238464	Chromatin interaction
ENSG00000203907	Chromatin interaction
ENSG00000231332	Chromatin interaction

Extended variants
information (count: 75 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:72)

rs_ID	r²[population]
rs10455092	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs10455273	0.96[ASN][1000 genomes]
rs10455274	0.96[ASN][1000 genomes]
rs1066687	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12153835	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12203663	0.96[ASN][1000 genomes]
rs12210531	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12216162	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12526643	0.91[AFR][1000 genomes];0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12529624	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12529658	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12530029	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12530079	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13194683	0.94[ASN][1000 genomes]
rs13212903	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13213885	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13219250	0.96[ASN][1000 genomes]
rs1555443	0.96[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1869559	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1970551	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1974368	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2124004	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2124006	0.89[CHB][hapmap];0.87[JPT][hapmap];0.81[ASN][1000 genomes]
rs2168113	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs2254630	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2603471	0.84[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs2797086	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28530192	0.96[ASN][1000 genomes]
rs2984129	0.96[ASN][1000 genomes]
rs34246858	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs34531450	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34637067	0.96[ASN][1000 genomes]
rs34821383	0.96[ASN][1000 genomes]
rs35664677	0.96[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4706533	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4706534	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4708041	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4708042	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs471270	0.99[ASN][1000 genomes]
rs471938	0.96[ASN][1000 genomes]
rs502107	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs502282	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs509406	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs510551	0.83[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs511219	0.95[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs512366	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs555779	0.95[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs57113415	0.86[ASN][1000 genomes]
rs573535	0.96[ASN][1000 genomes]
rs576229	0.95[CHB][hapmap];1.00[JPT][hapmap];0.93[ASN][1000 genomes]
rs579736	0.95[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs61493410	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62438232	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438233	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438235	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62438239	0.92[ASN][1000 genomes]
rs66984567	0.96[ASN][1000 genomes]
rs6923111	0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6923734	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7382700	0.97[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7740081	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7742847	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7743609	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7744174	0.98[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7758047	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7759043	0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7759315	0.95[CHB][hapmap];1.00[JPT][hapmap];0.82[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7764719	0.91[ASN][1000 genomes]
rs7765618	0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7769905	0.95[CHB][hapmap];0.88[JPT][hapmap];0.90[ASN][1000 genomes]
rs9800483	0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9800824	0.92[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv1022151	chr6:73876795-73996828	Weak transcription Active TSS Flanking Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases
3	nsv538304	chr6:73876795-73996828	Flanking Active TSS Weak transcription Genic enhancers Enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	23 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12208781	RP11-398K22.12	cis	Skin Sun Exposed Lower leg	GTEx
rs12208781	EIF3EP1	cis	Skin Sun Exposed Lower leg	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:73973400-73986400	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr6:73973400-74000400	Weak transcription	Aorta	Aorta
3	chr6:73973600-74018600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr6:73973600-74018600	Weak transcription	A549	lung
5	chr6:73973600-74018800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr6:73973800-73995600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr6:73973800-73995600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr6:73973800-74000400	Weak transcription	H9 Cell Line	embryonic stem cell
9	chr6:73974000-73995600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr6:73974000-74000400	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr6:73974000-74009000	Weak transcription	HSMM	muscle
12	chr6:73974000-74018400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
13	chr6:73974200-73992600	Weak transcription	Colon Smooth Muscle	Colon
14	chr6:73974400-73986600	Weak transcription	Pancreas	Pancrea
15	chr6:73974400-73986800	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr6:73974400-73986800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr6:73974400-73986800	Weak transcription	Spleen	Spleen
18	chr6:73974400-73987000	Weak transcription	Primary B cells from cord blood	blood
19	chr6:73974400-74000400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
20	chr6:73974400-74000400	Weak transcription	NHDF-Ad	bronchial
21	chr6:73974400-74008800	Weak transcription	NH-A	brain
22	chr6:73974400-74009400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr6:73974600-73986400	Weak transcription	Gastric	stomach
24	chr6:73974600-73986600	Weak transcription	Primary T cells fromperipheralblood	blood
25	chr6:73974600-73987000	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr6:73974600-73992600	Weak transcription	Brain Angular Gyrus	brain
27	chr6:73974600-74008600	Weak transcription	Brain Cingulate Gyrus	brain
28	chr6:73974800-73986400	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr6:73974800-73988400	Weak transcription	Brain Hippocampus Middle	brain
30	chr6:73974800-73992000	Weak transcription	GM12878-XiMat	blood
31	chr6:73974800-73994400	Weak transcription	NHLF	lung
32	chr6:73974800-73995600	Weak transcription	Hela-S3	cervix
33	chr6:73974800-74000400	Weak transcription	Brain Anterior Caudate	brain
34	chr6:73974800-74008600	Weak transcription	Brain Inferior Temporal Lobe	brain
35	chr6:73976200-73986400	Strong transcription	Dnd41	blood
36	chr6:73977400-74008800	Weak transcription	Fetal Brain Male	brain
37	chr6:73978000-73986800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
38	chr6:73979000-73991800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr6:73979200-74004400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr6:73980400-73986400	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
41	chr6:73980600-73986400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr6:73980600-73991000	Strong transcription	Fetal Stomach	stomach
43	chr6:73982400-73987200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
44	chr6:73982400-73988600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr6:73983600-73986400	Strong transcription	Fetal Brain Female	brain
46	chr6:73983800-74018600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr6:73984400-74000200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr6:73984400-74018600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
49	chr6:73984600-73992400	Weak transcription	K562	blood
50	chr6:73984600-74002200	Weak transcription	Primary T cells from cord blood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links