Variant report

Variant	rs17071566
Chromosome Location	chr13:80108625-80108626
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 73 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10492579	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10507899	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs1335373	0.92[EUR][1000 genomes]
rs1335374	0.88[EUR][1000 genomes]
rs1414157	1.00[EUR][1000 genomes]
rs17071385	1.00[CEU][hapmap]
rs17071415	1.00[CEU][hapmap]
rs17071499	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes]
rs17071532	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs17071549	1.00[CEU][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes]
rs17071558	1.00[CEU][hapmap];0.92[EUR][1000 genomes]
rs17071574	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17071585	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[EUR][1000 genomes]
rs17071627	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17071632	0.92[EUR][1000 genomes]
rs41288268	0.92[EUR][1000 genomes]
rs56711390	1.00[EUR][1000 genomes]
rs57032852	1.00[EUR][1000 genomes]
rs57929179	0.96[EUR][1000 genomes]
rs58056613	0.88[EUR][1000 genomes]
rs58069884	0.82[EUR][1000 genomes]
rs58406632	1.00[EUR][1000 genomes]
rs59165380	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs59381369	0.92[EUR][1000 genomes]
rs59755477	0.80[EUR][1000 genomes]
rs59783325	1.00[EUR][1000 genomes]
rs60126328	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61318325	0.96[EUR][1000 genomes]
rs61676417	1.00[EUR][1000 genomes]
rs6563107	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[TSI][hapmap]
rs6563117	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7317409	0.92[EUR][1000 genomes]
rs7317511	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7318854	0.92[EUR][1000 genomes]
rs7327148	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs7329633	0.84[EUR][1000 genomes]
rs7331979	1.00[CEU][hapmap]
rs7335191	0.88[EUR][1000 genomes]
rs7338043	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs73548951	0.92[EUR][1000 genomes]
rs73548955	0.92[EUR][1000 genomes]
rs73551558	0.92[EUR][1000 genomes]
rs73551595	1.00[EUR][1000 genomes]
rs73551596	1.00[EUR][1000 genomes]
rs73551597	1.00[EUR][1000 genomes]
rs73551601	1.00[EUR][1000 genomes]
rs73551602	1.00[EUR][1000 genomes]
rs73553403	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73553418	0.96[EUR][1000 genomes]
rs73553424	1.00[EUR][1000 genomes]
rs73553431	1.00[EUR][1000 genomes]
rs73553447	1.00[EUR][1000 genomes]
rs73553448	0.96[EUR][1000 genomes]
rs73553473	1.00[EUR][1000 genomes]
rs73553481	0.96[EUR][1000 genomes]
rs73553499	0.92[EUR][1000 genomes]
rs73555409	0.88[EUR][1000 genomes]
rs73555411	0.92[EUR][1000 genomes]
rs73555415	0.92[EUR][1000 genomes]
rs7491258	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.97[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7981574	1.00[EUR][1000 genomes]
rs7984159	0.93[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7984598	0.91[AFR][1000 genomes];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs7985220	0.82[EUR][1000 genomes]
rs7985697	0.92[EUR][1000 genomes]
rs7990190	1.00[EUR][1000 genomes]
rs7990464	1.00[EUR][1000 genomes]
rs7992181	1.00[CEU][hapmap]
rs7997554	1.00[CEU][hapmap];0.88[EUR][1000 genomes]
rs7998452	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs8000870	1.00[CEU][hapmap];0.92[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	nsv523979	chr13:79979679-80120263	Strong transcription Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv916983	chr13:80065879-80249702	Weak transcription Enhancers Genic enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:91 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr13:80066800-80122800	Weak transcription	Esophagus	oesophagus
2	chr13:80083000-80120000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
3	chr13:80083000-80122800	Weak transcription	Stomach Mucosa	stomach
4	chr13:80087400-80134000	Weak transcription	Aorta	Aorta
5	chr13:80087400-80134600	Weak transcription	Pancreas	Pancrea
6	chr13:80089400-80118400	Weak transcription	Small Intestine	intestine
7	chr13:80090600-80112000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr13:80092200-80109400	Weak transcription	Pancreatic Islets	Pancreatic Islet
9	chr13:80093000-80110200	Weak transcription	Cortex derived primary cultured neurospheres	brain
10	chr13:80093400-80112800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr13:80093800-80109800	Weak transcription	H1 Cell Line	embryonic stem cell
12	chr13:80095600-80109000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr13:80095600-80109000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr13:80097000-80109200	Weak transcription	Primary T cells fromperipheralblood	blood
15	chr13:80097000-80110400	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr13:80097000-80112400	Weak transcription	Thymus	Thymus
17	chr13:80097200-80112400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr13:80097200-80122800	Weak transcription	Fetal Lung	lung
19	chr13:80097400-80121800	Weak transcription	Lung	lung
20	chr13:80097800-80110800	Weak transcription	Fetal Intestine Small	intestine
21	chr13:80098000-80112600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr13:80098200-80111000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr13:80098400-80114200	Weak transcription	Placenta Amnion	Placenta Amnion
24	chr13:80098400-80123200	Weak transcription	Fetal Kidney	kidney
25	chr13:80098600-80135000	Weak transcription	Placenta	Placenta
26	chr13:80098800-80109800	Weak transcription	Skeletal Muscle Female	skeletal muscle
27	chr13:80099400-80112000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
28	chr13:80099400-80115600	Weak transcription	Skeletal Muscle Male	skeletal muscle
29	chr13:80099400-80133200	Weak transcription	Psoas Muscle	Psoas
30	chr13:80099600-80112000	Weak transcription	Adipose Nuclei	Adipose
31	chr13:80099800-80113600	Weak transcription	GM12878-XiMat	blood
32	chr13:80100400-80121600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr13:80100600-80136400	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr13:80100800-80133200	Weak transcription	Hela-S3	cervix
35	chr13:80101000-80123400	Weak transcription	HMEC	breast
36	chr13:80101800-80110800	Weak transcription	Sigmoid Colon	Sigmoid Colon
37	chr13:80101800-80133200	Weak transcription	Primary T cells from cord blood	blood
38	chr13:80102200-80133600	Weak transcription	Gastric	stomach
39	chr13:80102400-80111800	Weak transcription	Left Ventricle	heart
40	chr13:80102400-80114200	Weak transcription	Fetal Muscle Trunk	muscle
41	chr13:80102400-80114400	Weak transcription	Right Ventricle	heart
42	chr13:80102400-80115400	Weak transcription	Fetal Muscle Leg	muscle
43	chr13:80103400-80111000	Weak transcription	Fetal Stomach	stomach
44	chr13:80104400-80112200	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr13:80104800-80133600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr13:80105800-80115800	Weak transcription	Brain Anterior Caudate	brain
47	chr13:80106000-80112000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
48	chr13:80106200-80109000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
49	chr13:80106200-80111000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
50	chr13:80106200-80111200	Weak transcription	Fetal Thymus	thymus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links