Variant report

Variant	rs1168298
Chromosome Location	chr12:66735695-66735696
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA1	chr12:66734639-66735757	PBDE	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000238528	TF binding region

Extended variants
information (count: 83 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs1027399	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1027400	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1027401	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1039056	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1060724	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10784525	0.89[EUR][1000 genomes]
rs1168290	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168291	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168292	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168293	0.96[EUR][1000 genomes]
rs1168294	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168295	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168296	0.98[EUR][1000 genomes]
rs1168297	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168299	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168300	0.88[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168301	0.98[EUR][1000 genomes]
rs1168302	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168303	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168304	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168305	0.90[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168306	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168307	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168308	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168309	0.90[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1168310	0.97[EUR][1000 genomes]
rs1168311	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168314	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168315	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168316	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168317	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1168318	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168319	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168320	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168321	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168322	0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1168325	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1168327	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168328	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168329	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168330	0.94[EUR][1000 genomes]
rs1168332	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168333	0.95[EUR][1000 genomes]
rs1168334	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1168338	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168339	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168340	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1168341	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168342	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168343	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168344	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168345	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168346	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168347	0.94[EUR][1000 genomes]
rs1168348	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1168351	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168352	0.98[EUR][1000 genomes]
rs1168353	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168356	0.98[EUR][1000 genomes]
rs1168357	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1168358	0.98[EUR][1000 genomes]
rs1177555	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1179889	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1183272	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1183274	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1184551	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1184552	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1185244	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1495497	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1795527	0.88[EUR][1000 genomes]
rs1795529	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2172881	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2951656	0.96[EUR][1000 genomes]
rs4762091	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61925898	0.85[EUR][1000 genomes]
rs6581677	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs6581678	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs903587	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs903589	0.97[EUR][1000 genomes]
rs903590	0.98[EUR][1000 genomes]
rs961049	0.94[EUR][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	nsv1052503	chr12:66293898-67269495	Weak transcription Flanking Active TSS Enhancers Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
2	nsv541515	chr12:66293898-67269495	Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1168298	HELB	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:66697200-66742200	Weak transcription	Placenta Amnion	Placenta Amnion
2	chr12:66704400-66741800	Weak transcription	Hela-S3	cervix
3	chr12:66710200-66792800	Weak transcription	Fetal Kidney	kidney
4	chr12:66715600-66736600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
5	chr12:66724200-66745400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr12:66725400-66746400	Weak transcription	Small Intestine	intestine
7	chr12:66725600-66742800	Weak transcription	Colon Smooth Muscle	Colon
8	chr12:66730200-66736000	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
9	chr12:66730200-66737000	Strong transcription	Primary T helper naive cells from peripheral blood	blood
10	chr12:66731600-66736000	Strong transcription	Primary neutrophils fromperipheralblood	blood
11	chr12:66732400-66735800	ZNF genes & repeats	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr12:66732400-66735800	Strong transcription	Rectal Smooth Muscle	rectum
13	chr12:66732400-66737400	ZNF genes & repeats	Primary hematopoietic stem cells	blood
14	chr12:66732400-66739200	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:66732800-66740600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr12:66733000-66737800	ZNF genes & repeats	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr12:66733400-66735800	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
18	chr12:66733400-66736200	ZNF genes & repeats	Fetal Lung	lung
19	chr12:66733400-66736400	ZNF genes & repeats	HUES64 Cell Line	embryonic stem cell
20	chr12:66733600-66735800	ZNF genes & repeats	Primary T helper naive cells fromperipheralblood	blood
21	chr12:66733600-66735800	ZNF genes & repeats	Liver	Liver
22	chr12:66733600-66735800	ZNF genes & repeats	Brain Anterior Caudate	brain
23	chr12:66733600-66736000	ZNF genes & repeats	Primary B cells from peripheral blood	blood
24	chr12:66733600-66736000	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
25	chr12:66733600-66736000	ZNF genes & repeats	Pancreatic Islets	Pancreatic Islet
26	chr12:66733600-66736200	ZNF genes & repeats	Primary T cells from cord blood	blood
27	chr12:66733600-66736200	ZNF genes & repeats	Brain Substantia Nigra	brain
28	chr12:66733600-66736800	ZNF genes & repeats	Fetal Adrenal Gland	Adrenal Gland
29	chr12:66733800-66738800	ZNF genes & repeats	Dnd41	blood
30	chr12:66733800-66739600	Weak transcription	Fetal Heart	heart
31	chr12:66734200-66736000	ZNF genes & repeats	Fetal Muscle Leg	muscle
32	chr12:66734200-66738200	ZNF genes & repeats	Primary hematopoietic stem cells short term culture	blood
33	chr12:66734400-66735800	ZNF genes & repeats	Pancreas	Pancrea
34	chr12:66734400-66735800	ZNF genes & repeats	Spleen	Spleen
35	chr12:66734400-66736000	ZNF genes & repeats	Primary monocytes fromperipheralblood	blood
36	chr12:66734400-66736800	ZNF genes & repeats	Left Ventricle	heart
37	chr12:66734400-66737400	ZNF genes & repeats	Fetal Intestine Small	intestine
38	chr12:66734600-66735800	ZNF genes & repeats	Fetal Muscle Trunk	muscle
39	chr12:66734600-66735800	ZNF genes & repeats	Lung	lung
40	chr12:66734600-66735800	ZNF genes & repeats	Ovary	ovary
41	chr12:66734600-66735800	Strong transcription	Thymus	Thymus
42	chr12:66734600-66736000	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
43	chr12:66734600-66737000	ZNF genes & repeats	Breast Myoepithelial Primary Cells	Breast
44	chr12:66734800-66735800	ZNF genes & repeats	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
45	chr12:66734800-66735800	ZNF genes & repeats	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
46	chr12:66734800-66735800	ZNF genes & repeats	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr12:66734800-66735800	ZNF genes & repeats	Sigmoid Colon	Sigmoid Colon
48	chr12:66734800-66736000	ZNF genes & repeats	ES-UCSF4 Cell Line	embryonic stem cell
49	chr12:66734800-66736200	Strong transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
50	chr12:66734800-66736200	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links