Variant report

Variant	rs7083399
Chromosome Location	chr10:97105133-97105134
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs10786203	0.80[AMR][1000 genomes];0.99[ASN][1000 genomes]
rs11188283	0.83[LWK][hapmap]
rs11188287	0.95[CHB][hapmap];0.89[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.92[MEX][hapmap];0.82[AMR][1000 genomes];0.95[ASN][1000 genomes]
rs1410602	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410603	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1410605	0.80[LWK][hapmap]
rs1536561	0.82[JPT][hapmap]
rs2148891	0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2274629	1.00[ASW][hapmap];0.90[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];0.95[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];0.96[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2274630	1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3758582	1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.99[ASN][1000 genomes]
rs4917685	0.80[LWK][hapmap]
rs6583994	0.99[AFR][1000 genomes];0.93[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6583995	0.82[CHD][hapmap]
rs7069047	0.85[CHB][hapmap];0.90[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7080061	0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.91[TSI][hapmap];0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7095858	0.90[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7096152	0.85[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];0.88[MKK][hapmap];0.89[TSI][hapmap];0.89[AMR][1000 genomes];0.84[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs726175	0.83[ASW][hapmap];0.86[LWK][hapmap];0.83[MKK][hapmap]
rs726176	1.00[ASW][hapmap];0.90[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.88[MEX][hapmap];1.00[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.93[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7920051	0.96[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[ASN][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	nsv529726	chr10:96632494-97106315	Strong transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7083399	KIF11	cis	parietal	SCAN
rs7083399	FGFBP3	cis	parietal	SCAN
rs7083399	PDLIM1	cis	cerebellum	SCAN

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:97070400-97139600	Weak transcription	Fetal Brain Male	brain
2	chr10:97079400-97106400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr10:97080000-97109600	Weak transcription	Fetal Lung	lung
4	chr10:97080400-97106200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
5	chr10:97087800-97115400	Weak transcription	Colonic Mucosa	Colon
6	chr10:97088000-97110600	Weak transcription	Duodenum Mucosa	Duodenum
7	chr10:97093200-97106400	Weak transcription	HUES64 Cell Line	embryonic stem cell
8	chr10:97094400-97106600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr10:97094600-97118000	Weak transcription	HSMM	muscle
10	chr10:97095000-97110600	Weak transcription	Rectal Mucosa Donor 31	rectum
11	chr10:97095000-97115200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr10:97096400-97108400	Weak transcription	Rectal Mucosa Donor 29	rectum
13	chr10:97096400-97110600	Weak transcription	H9 Cell Line	embryonic stem cell
14	chr10:97096600-97110600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
15	chr10:97096800-97110600	Weak transcription	Psoas Muscle	Psoas
16	chr10:97097000-97106200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
17	chr10:97097800-97110600	Weak transcription	Right Atrium	heart
18	chr10:97097800-97116000	Weak transcription	Spleen	Spleen
19	chr10:97099200-97106600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
20	chr10:97099200-97106600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr10:97099200-97106600	Weak transcription	HUES48 Cell Line	embryonic stem cell
22	chr10:97099200-97106800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr10:97099200-97108400	Weak transcription	Gastric	stomach
24	chr10:97099200-97110600	Weak transcription	Lung	lung
25	chr10:97099200-97110800	Weak transcription	Fetal Intestine Small	intestine
26	chr10:97099200-97113400	Weak transcription	Ovary	ovary
27	chr10:97099200-97115200	Weak transcription	Esophagus	oesophagus
28	chr10:97099200-97129200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
29	chr10:97099400-97106600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr10:97099400-97106600	Weak transcription	Pancreas	Pancrea
31	chr10:97099400-97110000	Weak transcription	HMEC	breast
32	chr10:97099400-97110200	Weak transcription	Brain Hippocampus Middle	brain
33	chr10:97099400-97111000	Weak transcription	Brain Substantia Nigra	brain
34	chr10:97099600-97105800	Weak transcription	GM12878-XiMat	blood
35	chr10:97100000-97106600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
36	chr10:97100600-97105200	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr10:97100800-97108600	Weak transcription	Sigmoid Colon	Sigmoid Colon
38	chr10:97101200-97105200	Weak transcription	Brain Germinal Matrix	brain
39	chr10:97101200-97106600	Weak transcription	Right Ventricle	heart
40	chr10:97101200-97108400	Weak transcription	Fetal Muscle Trunk	muscle
41	chr10:97101400-97106600	Weak transcription	Fetal Heart	heart
42	chr10:97101600-97108600	Strong transcription	Stomach Smooth Muscle	stomach
43	chr10:97102000-97106400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
44	chr10:97102000-97108400	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr10:97102200-97106400	Strong transcription	Fetal Stomach	stomach
46	chr10:97102200-97136400	Weak transcription	Fetal Kidney	kidney
47	chr10:97102400-97106600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr10:97102400-97108400	Weak transcription	Rectal Smooth Muscle	rectum
49	chr10:97103200-97105400	Strong transcription	Fetal Intestine Large	intestine
50	chr10:97103400-97106000	Strong transcription	Skeletal Muscle Male	skeletal muscle

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links