Variant report

Variant	rs12490383
Chromosome Location	chr3:47494157-47494158
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	chr3:47490214..47492275-chr3:47492500..47494353,2	K562	blood:
2	chr3:47490125..47492275-chr3:47492500..47495080,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10490798	1.00[CEU][hapmap]
rs10865946	0.81[CHB][hapmap]
rs11130128	0.84[ASN][1000 genomes]
rs11130129	0.87[JPT][hapmap];0.84[ASN][1000 genomes]
rs12495169	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12632132	0.80[ASN][1000 genomes]
rs13059519	0.83[JPT][hapmap]
rs17080872	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.87[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2101247	0.84[ASN][1000 genomes]
rs2240796	1.00[CEU][hapmap];0.87[AFR][1000 genomes]
rs4858893	0.80[CHB][hapmap];0.84[JPT][hapmap]
rs4858894	0.87[JPT][hapmap];0.83[ASN][1000 genomes]
rs60369822	0.81[ASN][1000 genomes]
rs6792488	0.80[ASN][1000 genomes]
rs7649234	0.83[ASN][1000 genomes]
rs811115	0.82[JPT][hapmap]
rs878659	0.81[ASN][1000 genomes]
rs922957	0.81[CHB][hapmap]
rs9683033	0.84[ASN][1000 genomes]
rs9683177	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:15 , 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	nsv511233	chr3:47484797-47494157	Weak transcription Strong transcription Flanking Active TSS Enhancers Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
3	nsv590212	chr3:47485029-47500662	Flanking Active TSS Enhancers ZNF genes & repeats Weak transcription Strong transcription Active TSS Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3461079	chr3:47488748-47495346	Weak transcription Enhancers ZNF genes & repeats Strong transcription Genic enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
5	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
6	esv3489698	chr3:47489548-47494546	Weak transcription Enhancers ZNF genes & repeats	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	esv3461077	chr3:47489973-47494321	Weak transcription Enhancers ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
8	esv3489693	chr3:47489973-47494471	Enhancers Weak transcription ZNF genes & repeats	Chromatin interactive region	n/a	inside rSNPs	diseases
9	esv1805720	chr3:47490712-47494157	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
10	esv1843116	chr3:47490712-47494157	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
11	esv1848900	chr3:47490712-47494157	Weak transcription Enhancers	Chromatin interactive region	n/a	inside rSNPs	diseases
12	esv1816532	chr3:47490712-47511698	Weak transcription ZNF genes & repeats Enhancers Genic enhancers Strong transcription Flanking Active TSS	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
13	esv1841538	chr3:47490712-47511698	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
14	esv1848062	chr3:47490712-47511698	Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
15	esv1849930	chr3:47490712-47511698	Enhancers Genic enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription	TF binding region Chromatin interactive region	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12490383	KLHL18	Cis_1M	lymphoblastoid	RTeQTL
rs12490383	KLHL18	cis	normal skin	skin_eQTL

Chromatin state (count:55 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:47476600-47514200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
2	chr3:47481400-47496000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:47481400-47500600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr3:47484000-47507800	Weak transcription	Primary B cells from cord blood	blood
5	chr3:47484000-47511200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr3:47484200-47511200	Weak transcription	Primary B cells from peripheral blood	blood
7	chr3:47484400-47497200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr3:47484600-47494200	Weak transcription	Primary T helper cells PMA-I stimulated	--
9	chr3:47484600-47497400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
10	chr3:47484600-47500600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr3:47484600-47514000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr3:47484600-47514200	Weak transcription	Primary T cells fromperipheralblood	blood
13	chr3:47484600-47514200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr3:47484600-47514200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:47484600-47514800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr3:47484800-47504400	Weak transcription	Primary T helper cells fromperipheralblood	blood
17	chr3:47484800-47504600	Weak transcription	Primary T cells from cord blood	blood
18	chr3:47484800-47514800	Weak transcription	Thymus	Thymus
19	chr3:47485000-47514800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
20	chr3:47485200-47502600	Weak transcription	K562	blood
21	chr3:47485400-47494200	Weak transcription	Ovary	ovary
22	chr3:47485400-47503200	Weak transcription	Gastric	stomach
23	chr3:47486000-47494200	Weak transcription	Left Ventricle	heart
24	chr3:47486000-47497200	Weak transcription	A549	lung
25	chr3:47486000-47497400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
26	chr3:47486000-47500200	Weak transcription	Fetal Intestine Large	intestine
27	chr3:47486000-47500400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr3:47486000-47504600	Weak transcription	Rectal Smooth Muscle	rectum
29	chr3:47486000-47516000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr3:47486000-47516000	Weak transcription	Small Intestine	intestine
31	chr3:47486000-47516000	Weak transcription	HSMM	muscle
32	chr3:47486200-47497200	Weak transcription	Hela-S3	cervix
33	chr3:47486200-47502600	Weak transcription	Rectal Mucosa Donor 31	rectum
34	chr3:47486200-47506000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr3:47486200-47516000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr3:47486600-47494400	Weak transcription	HepG2	liver
37	chr3:47486600-47500600	Weak transcription	Skeletal Muscle Male	skeletal muscle
38	chr3:47487000-47502400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr3:47487400-47497600	Weak transcription	Liver	Liver
40	chr3:47489200-47500400	Weak transcription	Fetal Intestine Small	intestine
41	chr3:47491000-47494400	Weak transcription	Pancreas	Pancrea
42	chr3:47492200-47494800	Enhancers	Psoas Muscle	Psoas
43	chr3:47492600-47494200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
44	chr3:47493400-47494200	Weak transcription	Esophagus	oesophagus
45	chr3:47493400-47496400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
46	chr3:47493400-47510800	Weak transcription	Spleen	Spleen
47	chr3:47493600-47494200	Enhancers	Fetal Heart	heart
48	chr3:47493600-47494200	Weak transcription	Stomach Mucosa	stomach
49	chr3:47493800-47494200	Weak transcription	Fetal Stomach	stomach
50	chr3:47494000-47494200	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links