Variant report

Variant	rs338894
Chromosome Location	chr5:145148433-145148434
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	KAP1	chr5:145148409-145148917	U2OS	brain:	n/a	n/a
2	TCF7L2	chr5:145148214-145149301	HEK293	kidney:	n/a	n/a

Variant related genes	Relation type
PRELID2	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs10463270	0.82[EUR][1000 genomes]
rs12173238	0.85[JPT][hapmap];0.87[ASN][1000 genomes]
rs1654149	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1821250	0.85[CEU][hapmap];0.90[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1897545	0.85[CEU][hapmap];0.87[GIH][hapmap];0.95[TSI][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs338884	0.85[CEU][hapmap]
rs338887	0.92[CEU][hapmap];0.95[TSI][hapmap];0.86[EUR][1000 genomes]
rs338888	0.90[TSI][hapmap]
rs338889	0.92[CEU][hapmap];0.80[EUR][1000 genomes]
rs338891	0.84[CHB][hapmap];0.90[EUR][1000 genomes]
rs338892	0.84[CEU][hapmap];0.82[EUR][1000 genomes]
rs338893	0.84[CEU][hapmap];0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs338895	0.92[CEU][hapmap];0.89[CHB][hapmap];0.82[CHD][hapmap];0.87[GIH][hapmap];0.93[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs338896	0.92[CEU][hapmap];0.95[TSI][hapmap];0.92[EUR][1000 genomes]
rs338897	0.92[CEU][hapmap];0.95[TSI][hapmap];0.90[EUR][1000 genomes]
rs4305683	0.81[GIH][hapmap];0.81[MEX][hapmap];0.90[TSI][hapmap]
rs4460183	0.90[CHB][hapmap];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4628045	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs582130	0.90[EUR][1000 genomes]
rs587224	0.85[CEU][hapmap];0.95[TSI][hapmap]
rs677498	0.95[TSI][hapmap];0.82[EUR][1000 genomes]
rs680626	0.82[EUR][1000 genomes]
rs6868309	0.90[CHB][hapmap];0.94[ASN][1000 genomes]
rs7734685	0.82[AMR][1000 genomes];0.85[EUR][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	nsv1021851	chr5:145106686-145187560	Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs338894	SPINK1	cis	cerebellum	SCAN

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr5:145105400-145179000	Weak transcription	Pancreas	Pancrea
2	chr5:145109400-145194400	Weak transcription	Colonic Mucosa	Colon
3	chr5:145111400-145166800	Weak transcription	K562	blood
4	chr5:145114000-145163400	Weak transcription	Small Intestine	intestine
5	chr5:145126800-145155000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
6	chr5:145131000-145156800	Weak transcription	Gastric	stomach
7	chr5:145133000-145154800	Weak transcription	Fetal Lung	lung
8	chr5:145133800-145154600	Weak transcription	Osteobl	bone
9	chr5:145137800-145154400	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr5:145138000-145157800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr5:145139000-145165400	Weak transcription	Duodenum Smooth Muscle	Duodenum
12	chr5:145140000-145157800	Weak transcription	Sigmoid Colon	Sigmoid Colon
13	chr5:145140400-145157200	Weak transcription	Left Ventricle	heart
14	chr5:145140600-145153800	Weak transcription	Ovary	ovary
15	chr5:145140600-145156000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr5:145141200-145194400	Weak transcription	Stomach Smooth Muscle	stomach
17	chr5:145141400-145148600	Weak transcription	Colon Smooth Muscle	Colon
18	chr5:145141600-145155600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr5:145142400-145162400	Weak transcription	Rectal Smooth Muscle	rectum
20	chr5:145144200-145149800	Weak transcription	Duodenum Mucosa	Duodenum
21	chr5:145144200-145155200	Weak transcription	HUVEC	blood vessel
22	chr5:145144200-145156800	Weak transcription	Right Ventricle	heart
23	chr5:145144800-145154800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr5:145145400-145152000	Weak transcription	Rectal Mucosa Donor 29	rectum
25	chr5:145147200-145154800	Weak transcription	Adipose Nuclei	Adipose
26	chr5:145147200-145155000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr5:145147400-145151400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
28	chr5:145147400-145153200	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr5:145147400-145153800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr5:145147400-145155000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr5:145147400-145155000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr5:145147400-145155000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
33	chr5:145147400-145156000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr5:145147400-145157000	Weak transcription	Fetal Stomach	stomach
35	chr5:145147400-145161800	Weak transcription	Lung	lung
36	chr5:145147600-145153000	Weak transcription	Primary hematopoietic stem cells	blood
37	chr5:145147600-145156800	Weak transcription	Fetal Intestine Small	intestine
38	chr5:145148200-145148600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
39	chr5:145148200-145148800	Enhancers	Fetal Heart	heart
40	chr5:145148200-145154600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr5:145148400-145154800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links