Variant report

Variant	rs12632132
Chromosome Location	chr3:47477019-47477020
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	chr3:47476704..47482785-chr3:47483976..47487326,5	K562	blood:

Variant related genes	Relation type
ENSG00000114650	Chromatin interaction

Extended variants
information (count: 82 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1038394	0.87[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs10865946	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11130127	0.81[EUR][1000 genomes]
rs11130128	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130129	0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130132	0.85[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11130133	0.81[EUR][1000 genomes]
rs11705957	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11711265	0.81[EUR][1000 genomes]
rs11711824	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11712445	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11716763	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11719877	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11914913	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11914932	0.82[EUR][1000 genomes]
rs11925823	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12486969	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12487736	0.98[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12489046	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12490058	0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12490383	0.80[ASN][1000 genomes]
rs12492433	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12497225	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12630641	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12636851	0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13059519	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs13064843	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13075233	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs13079098	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1531875	0.97[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17411375	0.81[EUR][1000 genomes]
rs17784882	0.83[EUR][1000 genomes]
rs1872164	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2062278	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2101247	0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2159400	0.80[EUR][1000 genomes]
rs2291298	0.82[EUR][1000 genomes]
rs295428	0.84[AMR][1000 genomes]
rs295449	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs295458	0.90[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs295461	0.88[AMR][1000 genomes]
rs3736177	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3816779	0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4241548	0.96[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858805	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858848	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs4858868	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4858888	0.82[EUR][1000 genomes]
rs4858894	0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs553989	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs56032309	0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs56351005	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs57346147	0.90[EUR][1000 genomes]
rs59586735	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60369822	0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs62246474	0.81[EUR][1000 genomes]
rs62248580	0.81[EUR][1000 genomes]
rs62248599	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62248603	0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs62248605	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs62260710	0.80[EUR][1000 genomes]
rs62260711	0.80[EUR][1000 genomes]
rs6765990	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6780013	0.82[EUR][1000 genomes]
rs6787422	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs6792461	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6792488	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6800271	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73081205	0.88[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7613282	0.80[EUR][1000 genomes]
rs7628631	0.82[EUR][1000 genomes]
rs7641010	0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7649234	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651194	0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7651762	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs807810	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs807931	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs878659	0.83[AFR][1000 genomes];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs922957	0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9683033	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9683177	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv876756	chr3:47002931-47586514	Strong transcription Enhancers Weak transcription Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	79 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12632132	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12632132	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47450400-47484800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:47461800-47478800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
3	chr3:47463000-47485200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr3:47463400-47477600	Strong transcription	Fetal Thymus	thymus
5	chr3:47463400-47484600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr3:47463600-47484800	Strong transcription	Primary T cells from cord blood	blood
7	chr3:47463800-47479400	Weak transcription	A549	lung
8	chr3:47464000-47484200	Weak transcription	Right Atrium	heart
9	chr3:47464800-47477200	Strong transcription	Fetal Muscle Trunk	muscle
10	chr3:47465400-47484600	Strong transcription	Primary T cells fromperipheralblood	blood
11	chr3:47465600-47484200	Strong transcription	Primary B cells from peripheral blood	blood
12	chr3:47469200-47484400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr3:47470000-47481200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
14	chr3:47471200-47477400	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr3:47471600-47479600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr3:47471800-47485000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr3:47472000-47482200	Strong transcription	Cortex derived primary cultured neurospheres	brain
18	chr3:47472000-47484600	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr3:47472400-47477200	Strong transcription	H1 Cell Line	embryonic stem cell
20	chr3:47472400-47484600	Strong transcription	Primary neutrophils fromperipheralblood	blood
21	chr3:47472400-47485200	Weak transcription	Fetal Brain Male	brain
22	chr3:47472800-47484400	Strong transcription	iPS-20b Cell Line	embryonic stem cell
23	chr3:47473000-47479400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr3:47473200-47483600	Weak transcription	Fetal Heart	heart
25	chr3:47473200-47487200	Weak transcription	HUVEC	blood vessel
26	chr3:47473400-47481000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
27	chr3:47474000-47481600	Strong transcription	Primary hematopoietic stem cells	blood
28	chr3:47474000-47483600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr3:47474600-47489600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr3:47475000-47478000	Genic enhancers	Fetal Intestine Small	intestine
31	chr3:47475000-47480000	Weak transcription	HMEC	breast
32	chr3:47475000-47484600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
33	chr3:47475800-47478000	Enhancers	Stomach Mucosa	stomach
34	chr3:47475800-47480400	Weak transcription	K562	blood
35	chr3:47475800-47481000	Weak transcription	Gastric	stomach
36	chr3:47475800-47481000	Weak transcription	Hela-S3	cervix
37	chr3:47475800-47482800	Weak transcription	NHDF-Ad	bronchial
38	chr3:47476000-47479400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr3:47476000-47480200	Weak transcription	Fetal Lung	lung
40	chr3:47476000-47483800	Weak transcription	Pancreatic Islets	Pancreatic Islet
41	chr3:47476000-47484200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
42	chr3:47476000-47484200	Weak transcription	Colonic Mucosa	Colon
43	chr3:47476000-47485800	Weak transcription	Fetal Kidney	kidney
44	chr3:47476200-47481000	Weak transcription	Osteobl	bone
45	chr3:47476400-47478600	Genic enhancers	Liver	Liver
46	chr3:47476600-47477800	Enhancers	Fetal Intestine Large	intestine
47	chr3:47476600-47477800	Weak transcription	Lung	lung
48	chr3:47476600-47478200	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr3:47476600-47478600	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr3:47476600-47479000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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