Variant report

Variant	rs1556086
Chromosome Location	chr13:97978485-97978486
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:11)

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];0.82[ASN][1000 genomes]
rs16954019	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]
rs59195107	0.91[AFR][1000 genomes];0.81[AMR][1000 genomes]
rs7333720	0.85[CEU][hapmap];1.00[CHB][hapmap];0.92[YRI][hapmap];0.82[ASN][1000 genomes]
rs7989373	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9556703	0.81[CHB][hapmap];0.89[JPT][hapmap]
rs9556710	0.82[ASN][1000 genomes]
rs9556711	0.85[CEU][hapmap];0.87[CHB][hapmap];0.80[CHD][hapmap]
rs9582126	0.82[CEU][hapmap]

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
rs1556086	STK24	cis	cerebellum	SCAN

Chromatin state (count:93 , 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	chr13:97954400-97986200	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr13:97955000-97987000	Weak transcription	Primary T helper cells fromperipheralblood	blood
5	chr13:97955200-97986800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
6	chr13:97959400-97988800	Weak transcription	Fetal Intestine Large	intestine
7	chr13:97961400-97987200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
8	chr13:97962000-97979200	Weak transcription	HUVEC	blood vessel
9	chr13:97962000-97991200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
10	chr13:97963000-97984400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr13:97965200-97985800	Weak transcription	Pancreatic Islets	Pancreatic Islet
12	chr13:97965600-97988800	Weak transcription	Primary hematopoietic stem cells	blood
13	chr13:97965800-97987200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
14	chr13:97967000-97980400	Weak transcription	Fetal Thymus	thymus
15	chr13:97967400-97991400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr13:97969200-97979200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr13:97969400-97981600	Weak transcription	Spleen	Spleen
18	chr13:97969400-97981800	Weak transcription	Esophagus	oesophagus
19	chr13:97969600-97982000	Weak transcription	Primary B cells from cord blood	blood
20	chr13:97969600-97987200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
21	chr13:97969800-97986600	Weak transcription	Primary B cells from peripheral blood	blood
22	chr13:97971400-97979800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr13:97971400-97981800	Weak transcription	Gastric	stomach
24	chr13:97971600-97979800	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr13:97971600-97981600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr13:97971600-97991400	Weak transcription	Stomach Mucosa	stomach
27	chr13:97971800-97979800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
28	chr13:97971800-97980200	Weak transcription	Placenta	Placenta
29	chr13:97971800-97980600	Weak transcription	Pancreas	Pancrea
30	chr13:97971800-97981600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr13:97971800-97986400	Weak transcription	Primary T cells from cord blood	blood
32	chr13:97971800-97986400	Weak transcription	Aorta	Aorta
33	chr13:97971800-97986400	Weak transcription	Rectal Mucosa Donor 29	rectum
34	chr13:97971800-97987200	Weak transcription	Sigmoid Colon	Sigmoid Colon
35	chr13:97971800-97987600	Weak transcription	Fetal Intestine Small	intestine
36	chr13:97971800-97987800	Weak transcription	Colonic Mucosa	Colon
37	chr13:97971800-97991800	Weak transcription	Small Intestine	intestine
38	chr13:97972000-97980000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr13:97972000-97987200	Weak transcription	Rectal Mucosa Donor 31	rectum
40	chr13:97972200-97980200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr13:97972400-97981800	Weak transcription	Liver	Liver
42	chr13:97972400-97986400	Weak transcription	Duodenum Mucosa	Duodenum
43	chr13:97973000-97979600	Enhancers	Brain Hippocampus Middle	brain
44	chr13:97973000-97983200	Enhancers	Brain Cingulate Gyrus	brain
45	chr13:97973200-97983400	Enhancers	Rectal Smooth Muscle	rectum
46	chr13:97974400-97979200	Weak transcription	A549	lung
47	chr13:97974600-97980200	Weak transcription	H1 Cell Line	embryonic stem cell
48	chr13:97974800-97979800	Weak transcription	Fetal Heart	heart
49	chr13:97974800-97980400	Enhancers	Stomach Smooth Muscle	stomach
50	chr13:97975000-97980200	Weak transcription	iPS-20b Cell Line	embryonic stem cell

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links