Variant report

Variant	rs12492433
Chromosome Location	chr3:47515557-47515558
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:47505383..47508183-chr3:47513358..47515947,2	K562	blood:
2	chr3:47514858..47522453-chr3:47552535..47558710,16	K562	blood:
3	chr3:47513969..47516839-chr3:47829270..47830805,2	K562	blood:

Variant related genes	Relation type
ENSG00000238350	Chromatin interaction
ENSG00000163832	Chromatin interaction

Extended variants
information (count: 74 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs1038394	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10865946	0.86[EUR][1000 genomes]
rs11130128	0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130129	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11130132	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11130133	0.90[EUR][1000 genomes]
rs11130137	0.87[EUR][1000 genomes]
rs11705957	0.85[EUR][1000 genomes]
rs11707895	0.87[EUR][1000 genomes]
rs11711265	0.90[EUR][1000 genomes]
rs11711824	0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11712445	0.86[EUR][1000 genomes]
rs11713413	0.84[EUR][1000 genomes]
rs11716763	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11719877	0.86[EUR][1000 genomes]
rs11914913	0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11914932	0.91[EUR][1000 genomes]
rs11925823	0.86[EUR][1000 genomes]
rs12486969	0.85[EUR][1000 genomes]
rs12487736	0.83[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12489046	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12490058	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12497225	0.86[EUR][1000 genomes]
rs12630641	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12632132	0.80[AFR][1000 genomes];0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12636851	0.88[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs13059519	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13064843	0.86[EUR][1000 genomes]
rs13075233	0.86[EUR][1000 genomes]
rs13079098	0.85[EUR][1000 genomes]
rs1531875	0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17784882	0.92[EUR][1000 genomes]
rs1872164	0.86[EUR][1000 genomes]
rs2062278	0.86[EUR][1000 genomes]
rs2101247	0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2291298	0.91[EUR][1000 genomes]
rs34634681	0.87[EUR][1000 genomes]
rs3736177	0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3816779	0.84[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4599332	0.86[EUR][1000 genomes]
rs4858805	0.84[EUR][1000 genomes]
rs4858848	0.83[EUR][1000 genomes]
rs4858856	0.89[EUR][1000 genomes]
rs4858868	0.88[EUR][1000 genomes]
rs4858894	0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs56032309	0.86[EUR][1000 genomes]
rs56351005	0.84[EUR][1000 genomes]
rs57346147	0.86[EUR][1000 genomes]
rs59586735	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs60369822	0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62248599	0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62248603	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62248605	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs62260710	0.89[EUR][1000 genomes]
rs62260711	0.89[EUR][1000 genomes]
rs62260741	0.84[EUR][1000 genomes]
rs6765990	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787422	0.86[EUR][1000 genomes]
rs6790763	0.86[EUR][1000 genomes]
rs6792461	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6792488	0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6800271	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs73081205	0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7628631	0.91[EUR][1000 genomes]
rs7641010	0.82[EUR][1000 genomes]
rs7649234	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7651194	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7651762	0.89[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs878659	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs922957	0.86[EUR][1000 genomes]
rs9683033	0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9683177	0.97[EUR][1000 genomes];0.93[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	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
2	nsv3806	chr3:47488784-47518133	Flanking Active TSS Active TSS Enhancers ZNF genes & repeats Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12492433	SETD2	Cis_1M	lymphoblastoid	RTeQTL
rs12492433	KLHL18	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
3	chr3:47486000-47516000	Weak transcription	HSMM	muscle
4	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
5	chr3:47497800-47516000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:47497800-47516000	Weak transcription	A549	lung
7	chr3:47497800-47516000	Weak transcription	NHDF-Ad	bronchial
8	chr3:47498800-47516000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
9	chr3:47501000-47516200	Weak transcription	Brain Cingulate Gyrus	brain
10	chr3:47501400-47516200	Weak transcription	HSMMtube	muscle
11	chr3:47502400-47516000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr3:47503200-47516000	Weak transcription	Brain Inferior Temporal Lobe	brain
13	chr3:47503400-47516000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr3:47504000-47516200	Weak transcription	Gastric	stomach
15	chr3:47505000-47516000	Weak transcription	Stomach Smooth Muscle	stomach
16	chr3:47505600-47516000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr3:47506800-47516200	Weak transcription	Fetal Lung	lung
18	chr3:47507200-47516000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:47507600-47516000	Weak transcription	Lung	lung
20	chr3:47507800-47516000	Weak transcription	HUVEC	blood vessel
21	chr3:47509000-47516000	Weak transcription	Right Ventricle	heart
22	chr3:47509200-47516000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:47509200-47516200	Weak transcription	Fetal Stomach	stomach
24	chr3:47510800-47516000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
25	chr3:47511000-47516000	Weak transcription	Primary B cells from cord blood	blood
26	chr3:47511600-47515800	Weak transcription	Primary B cells from peripheral blood	blood
27	chr3:47511800-47515600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr3:47512000-47516000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:47512000-47516000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
30	chr3:47513000-47516000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr3:47513200-47516000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr3:47513600-47516000	Weak transcription	Muscle Satellite Cultured Cells	--
33	chr3:47513800-47516000	Weak transcription	Fetal Muscle Trunk	muscle
34	chr3:47514000-47516200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr3:47514000-47516200	Enhancers	Pancreas	Pancrea
36	chr3:47514000-47516400	Enhancers	Sigmoid Colon	Sigmoid Colon
37	chr3:47514200-47515800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
38	chr3:47514200-47516000	Enhancers	Breast Myoepithelial Primary Cells	Breast
39	chr3:47514200-47516200	Enhancers	Primary T cells fromperipheralblood	blood
40	chr3:47514200-47516200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
41	chr3:47514200-47516200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
42	chr3:47514200-47516200	Enhancers	Left Ventricle	heart
43	chr3:47514200-47516600	Enhancers	Spleen	Spleen
44	chr3:47514600-47515600	Enhancers	Primary T cells from cord blood	blood
45	chr3:47514600-47515600	Enhancers	NHEK	skin
46	chr3:47514600-47516000	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr3:47514600-47516000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
48	chr3:47514600-47516000	Enhancers	Fetal Brain Female	brain
49	chr3:47514600-47516000	Enhancers	Fetal Intestine Large	intestine
50	chr3:47514600-47516000	Enhancers	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links