Variant report

Variant	rs16954019
Chromosome Location	chr13:97970886-97970887
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	chr13:97964833..97966698-chr13:97969721..97972103,2	K562	blood:

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11069259	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap]
rs11838553	0.85[CEU][hapmap];1.00[CHB][hapmap];0.83[CHD][hapmap];0.81[ASN][1000 genomes]
rs1463791	0.89[ASW][hapmap];0.89[LWK][hapmap];0.83[YRI][hapmap];0.87[AFR][1000 genomes]
rs1556086	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.82[MEX][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2173036	0.82[CEU][hapmap];0.91[LWK][hapmap];0.84[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7333720	0.85[CEU][hapmap];1.00[CHB][hapmap];0.81[ASN][1000 genomes]
rs73557675	0.97[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs7989373	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9556703	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9556710	0.81[ASN][1000 genomes]
rs9556711	0.85[CEU][hapmap];0.87[CHB][hapmap];0.81[CHD][hapmap]
rs9582125	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9582126	0.83[ASW][hapmap];0.82[CEU][hapmap];0.91[LWK][hapmap];0.85[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9584550	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs9584551	0.84[AFR][1000 genomes];0.82[AMR][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	nsv832694	chr13:97930561-98137882	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs16954019	STK24	cis	cerebellum	SCAN

Chromatin state (count:87 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:97925800-97987200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr13:97942800-97995200	Weak transcription	Thymus	Thymus
3	chr13:97948600-97971600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr13:97950000-97971200	Weak transcription	Stomach Mucosa	stomach
5	chr13:97954400-97986200	Weak transcription	Primary T cells fromperipheralblood	blood
6	chr13:97955000-97987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
7	chr13:97955200-97986800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr13:97955400-97971400	Weak transcription	Rectal Mucosa Donor 31	rectum
9	chr13:97959000-97971200	Weak transcription	Duodenum Mucosa	Duodenum
10	chr13:97959400-97988800	Weak transcription	Fetal Intestine Large	intestine
11	chr13:97961000-97973800	Weak transcription	NHEK	skin
12	chr13:97961400-97975200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
13	chr13:97961400-97987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
14	chr13:97961600-97971000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
15	chr13:97961600-97971200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
16	chr13:97961600-97975400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr13:97961800-97971000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
18	chr13:97961800-97975200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr13:97961800-97977600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
20	chr13:97961800-97978000	Weak transcription	HMEC	breast
21	chr13:97962000-97971000	Weak transcription	Gastric	stomach
22	chr13:97962000-97979200	Weak transcription	HUVEC	blood vessel
23	chr13:97962000-97991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr13:97962400-97971000	Weak transcription	NH-A	brain
25	chr13:97962400-97978200	Weak transcription	K562	blood
26	chr13:97962600-97971200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr13:97963000-97972600	Enhancers	Brain Substantia Nigra	brain
28	chr13:97963000-97984400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
29	chr13:97963600-97977000	Weak transcription	Hela-S3	cervix
30	chr13:97965000-97972600	Enhancers	Brain Hippocampus Middle	brain
31	chr13:97965200-97985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
32	chr13:97965600-97988800	Weak transcription	Primary hematopoietic stem cells	blood
33	chr13:97965800-97971600	Genic enhancers	Breast Myoepithelial Primary Cells	Breast
34	chr13:97965800-97987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
35	chr13:97967000-97980400	Weak transcription	Fetal Thymus	thymus
36	chr13:97967400-97972600	Enhancers	Colon Smooth Muscle	Colon
37	chr13:97967400-97991400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr13:97967600-97972600	Enhancers	Brain Cingulate Gyrus	brain
39	chr13:97968000-97972000	Enhancers	Brain Inferior Temporal Lobe	brain
40	chr13:97968000-97972600	Enhancers	Brain Anterior Caudate	brain
41	chr13:97968200-97972600	Enhancers	Fetal Muscle Leg	muscle
42	chr13:97968400-97971800	Genic enhancers	Fetal Stomach	stomach
43	chr13:97968600-97971000	Weak transcription	Placenta Amnion	Placenta Amnion
44	chr13:97968600-97971200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:97969000-97971000	Weak transcription	Primary T cells from cord blood	blood
46	chr13:97969000-97971600	Weak transcription	Aorta	Aorta
47	chr13:97969200-97971000	Weak transcription	Liver	Liver
48	chr13:97969200-97971200	Enhancers	Skeletal Muscle Male	skeletal muscle
49	chr13:97969200-97972000	Enhancers	Fetal Lung	lung
50	chr13:97969200-97972000	Enhancers	Skeletal Muscle Female	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links