Variant report

Variant	rs992583
Chromosome Location	chr13:52278559-52278560
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs12856726	0.82[MEX][hapmap]
rs1885855	0.87[AFR][1000 genomes];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1923874	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4456399	0.87[ASW][hapmap];0.96[CEU][hapmap];0.91[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];0.95[JPT][hapmap];0.89[LWK][hapmap];1.00[TSI][hapmap];0.85[AFR][1000 genomes];0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4533167	0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.86[ASN][1000 genomes]
rs4943008	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.80[YRI][hapmap];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs4943014	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6561644	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7320201	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7327107	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7984225	0.88[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.89[LWK][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7988297	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7990679	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.97[TSI][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9285179	0.94[ASW][hapmap];0.81[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.98[LWK][hapmap];0.95[MEX][hapmap];0.99[MKK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[ASN][1000 genomes]
rs9526792	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.99[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9535716	0.85[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.85[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs9535720	0.96[CEU][hapmap];0.86[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs9568642	0.87[MEX][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	nsv832612	chr13:52176983-52362525	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs992583	TNNI2	trans	parietal	SCAN
rs992583	NCRNA00282	cis	parietal	SCAN

Chromatin state (count:76 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:52247600-52300200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
2	chr13:52247600-52300200	Weak transcription	Fetal Lung	lung
3	chr13:52249400-52307600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr13:52254600-52293000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
5	chr13:52254600-52301800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr13:52258000-52280400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr13:52263400-52295600	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr13:52264000-52300000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
9	chr13:52264200-52280800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr13:52269800-52278800	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr13:52270400-52279000	Weak transcription	Esophagus	oesophagus
12	chr13:52270400-52293200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
13	chr13:52270800-52301600	Weak transcription	H1 Cell Line	embryonic stem cell
14	chr13:52271200-52301800	Weak transcription	HUES64 Cell Line	embryonic stem cell
15	chr13:52271800-52281400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
16	chr13:52272200-52288800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr13:52272400-52279600	Weak transcription	Brain Angular Gyrus	brain
18	chr13:52272400-52287600	Weak transcription	NHDF-Ad	bronchial
19	chr13:52272400-52288800	Weak transcription	NHLF	lung
20	chr13:52273400-52279200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr13:52273400-52291800	Weak transcription	Brain Anterior Caudate	brain
22	chr13:52273600-52279000	Weak transcription	Gastric	stomach
23	chr13:52273600-52291400	Weak transcription	Brain Hippocampus Middle	brain
24	chr13:52273600-52293000	Weak transcription	Right Atrium	heart
25	chr13:52273600-52293200	Weak transcription	Left Ventricle	heart
26	chr13:52273600-52295200	Weak transcription	Right Ventricle	heart
27	chr13:52273600-52295600	Weak transcription	Pancreas	Pancrea
28	chr13:52273600-52295800	Weak transcription	Spleen	Spleen
29	chr13:52274000-52279200	Weak transcription	Aorta	Aorta
30	chr13:52274000-52295600	Weak transcription	Ovary	ovary
31	chr13:52274000-52300400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
32	chr13:52275200-52284200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr13:52275800-52279000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr13:52276000-52278600	Weak transcription	HUES6 Cell Line	embryonic stem cell
35	chr13:52276400-52280800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
36	chr13:52276400-52285000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
37	chr13:52276400-52295400	Weak transcription	Adipose Nuclei	Adipose
38	chr13:52276600-52301800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr13:52276800-52288800	Weak transcription	Primary neutrophils fromperipheralblood	blood
40	chr13:52277000-52281600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr13:52277000-52283600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr13:52277000-52300000	Weak transcription	Primary T helper cells PMA-I stimulated	--
43	chr13:52277200-52279000	Weak transcription	Cortex derived primary cultured neurospheres	brain
44	chr13:52277400-52279600	Strong transcription	Primary T helper cells fromperipheralblood	blood
45	chr13:52277400-52281800	Weak transcription	Fetal Muscle Leg	muscle
46	chr13:52277600-52279200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr13:52277600-52279600	Strong transcription	NH-A	brain
48	chr13:52277600-52280400	Strong transcription	HepG2	liver
49	chr13:52277800-52278800	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
50	chr13:52277800-52279000	Enhancers	Primary B cells from cord blood	blood

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