Variant report

Variant	rs14137
Chromosome Location	chr1:215793834-215793835
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12058673	0.87[YRI][hapmap]
rs2677111	0.91[CEU][hapmap];0.90[CHB][hapmap];0.91[CHD][hapmap];0.90[GIH][hapmap];0.93[TSI][hapmap];0.85[EUR][1000 genomes]
rs2677117	0.95[CEU][hapmap];0.95[CHB][hapmap];0.91[CHD][hapmap];0.85[JPT][hapmap];0.87[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2677118	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2797224	0.85[CHB][hapmap]
rs2797229	0.91[CEU][hapmap];0.81[CHB][hapmap];0.80[CHD][hapmap];0.88[GIH][hapmap];0.88[TSI][hapmap];0.81[EUR][1000 genomes]
rs2797254	0.88[EUR][1000 genomes]
rs2797386	0.85[CHB][hapmap]
rs2797389	0.80[YRI][hapmap]
rs2797393	1.00[ASW][hapmap];0.95[CEU][hapmap];0.85[GIH][hapmap];0.90[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.93[AMR][1000 genomes];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	esv1796390	chr1:215561548-215799074	Weak transcription Bivalent/Poised TSS Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	9 gene(s)	inside rSNPs	diseases
2	nsv430324	chr1:215649163-216082605	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs14137	KCTD3	cis	cerebellar cortex	BrainEAC
rs14137	KCTD3	cis	brain	BrainEAC

Chromatin state (count:110 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:215741800-215809800	Weak transcription	Colonic Mucosa	Colon
2	chr1:215750000-215805000	Weak transcription	Lung	lung
3	chr1:215750200-215795400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr1:215750200-215796000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr1:215750200-215804400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:215750200-215809200	Weak transcription	Gastric	stomach
7	chr1:215755800-215804800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr1:215773800-215798600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
9	chr1:215774000-215795200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr1:215779400-215799200	Weak transcription	Psoas Muscle	Psoas
11	chr1:215780000-215794000	Weak transcription	Primary B cells from peripheral blood	blood
12	chr1:215781000-215797200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr1:215781200-215794800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr1:215781200-215797400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr1:215782200-215799400	Weak transcription	Fetal Heart	heart
16	chr1:215782800-215797200	Weak transcription	Dnd41	blood
17	chr1:215783000-215798800	Weak transcription	Brain Inferior Temporal Lobe	brain
18	chr1:215784200-215795200	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:215784800-215796600	Weak transcription	Spleen	Spleen
20	chr1:215786600-215809400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr1:215786800-215794000	Weak transcription	Thymus	Thymus
22	chr1:215786800-215796200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
23	chr1:215786800-215797400	Weak transcription	Fetal Brain Female	brain
24	chr1:215786800-215798200	Weak transcription	Brain Cingulate Gyrus	brain
25	chr1:215786800-215799000	Weak transcription	Small Intestine	intestine
26	chr1:215786800-215801000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr1:215787000-215796000	Weak transcription	Placenta Amnion	Placenta Amnion
28	chr1:215787200-215795600	Weak transcription	Primary B cells from cord blood	blood
29	chr1:215787200-215796400	Weak transcription	Colon Smooth Muscle	Colon
30	chr1:215787200-215798400	Weak transcription	Primary T cells from cord blood	blood
31	chr1:215787200-215800600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr1:215787200-215810200	Weak transcription	Pancreatic Islets	Pancreatic Islet
33	chr1:215787400-215794400	Weak transcription	Primary T helper cells PMA-I stimulated	--
34	chr1:215787400-215797000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr1:215787600-215801800	Weak transcription	Skeletal Muscle Male	skeletal muscle
36	chr1:215788400-215796000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr1:215788800-215794200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr1:215789000-215794600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr1:215789000-215797000	Strong transcription	Fetal Intestine Large	intestine
40	chr1:215789000-215797000	Strong transcription	Fetal Muscle Trunk	muscle
41	chr1:215789000-215799200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr1:215789200-215794400	Strong transcription	Duodenum Mucosa	Duodenum
43	chr1:215789200-215794800	Strong transcription	HepG2	liver
44	chr1:215789200-215796000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
45	chr1:215789200-215797000	Strong transcription	Adipose Nuclei	Adipose
46	chr1:215789200-215797400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
47	chr1:215789800-215794400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
48	chr1:215789800-215794600	Strong transcription	Duodenum Smooth Muscle	Duodenum
49	chr1:215790000-215794600	Strong transcription	Rectal Mucosa Donor 29	rectum
50	chr1:215790200-215794800	Strong transcription	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links