Variant report

Variant	rs2805793
Chromosome Location	chr9:100353171-100353172
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	chr9:100184396..100186994-chr9:100352263..100355014,2	K562	blood:

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10123528	1.00[JPT][hapmap]
rs10982745	0.85[CHD][hapmap]
rs16922598	1.00[JPT][hapmap]
rs2149984	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes]
rs2254733	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2773343	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.97[TSI][hapmap];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2773344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2773349	0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2773350	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2773358	0.91[EUR][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	0.91[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.88[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.86[CEU][hapmap];0.81[EUR][1000 genomes]
rs2805785	1.00[CEU][hapmap];0.95[EUR][1000 genomes]
rs2805786	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805787	0.95[EUR][1000 genomes]
rs2805788	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805792	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.86[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2805804	0.81[AMR][1000 genomes]
rs2805805	0.84[AMR][1000 genomes]
rs2805831	0.82[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.87[TSI][hapmap]
rs2805835	1.00[JPT][hapmap]
rs2808682	1.00[JPT][hapmap]
rs7863516	0.82[ASN][1000 genomes]
rs932916	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.82[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1039240	chr9:100292680-100415269	Weak transcription Strong transcription Genic enhancers Flanking Active TSS Enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
2	nsv540179	chr9:100292680-100415269	Genic enhancers Strong transcription Weak transcription Active TSS Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	27 gene(s)	inside rSNPs	diseases
3	nsv893610	chr9:100324086-100496160	Active TSS Strong transcription Enhancers ZNF genes & repeats Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	32 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs2805793	TMOD1	cis	multi-tissue	Pritchard
rs2805793	TBC1D2	cis	parietal	SCAN
rs2805793	TMOD1,TSTD2	cis	cerebellar cortex	BrainEAC
rs2805793	TMOD1	cis	cerebellum	SCAN
rs2805793	C9orf89	cis	cerebellum	SCAN
rs2805793	ZNF367	cis	parietal	SCAN

Chromatin state (count:36 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100333600-100361800	Weak transcription	Gastric	stomach
2	chr9:100334200-100356000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr9:100334400-100356000	Weak transcription	Brain Cingulate Gyrus	brain
4	chr9:100334400-100356400	Weak transcription	HSMMtube	muscle
5	chr9:100334600-100353600	Weak transcription	Colon Smooth Muscle	Colon
6	chr9:100334800-100355600	Weak transcription	Rectal Smooth Muscle	rectum
7	chr9:100335600-100356600	Weak transcription	Brain Angular Gyrus	brain
8	chr9:100336200-100356200	Weak transcription	Aorta	Aorta
9	chr9:100336200-100360000	Weak transcription	Brain Substantia Nigra	brain
10	chr9:100338200-100356200	Weak transcription	Brain Inferior Temporal Lobe	brain
11	chr9:100338200-100356800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr9:100338400-100353400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr9:100338400-100356000	Weak transcription	Brain Anterior Caudate	brain
14	chr9:100338400-100361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr9:100338600-100353200	Weak transcription	Fetal Muscle Leg	muscle
16	chr9:100338600-100360800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr9:100341200-100358400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
18	chr9:100341600-100353600	Weak transcription	Ovary	ovary
19	chr9:100341600-100356000	Weak transcription	Right Atrium	heart
20	chr9:100342200-100353200	Weak transcription	Skeletal Muscle Female	skeletal muscle
21	chr9:100342400-100353200	Weak transcription	Psoas Muscle	Psoas
22	chr9:100342400-100353400	Weak transcription	Stomach Smooth Muscle	stomach
23	chr9:100342400-100353600	Weak transcription	Fetal Heart	heart
24	chr9:100342400-100355800	Weak transcription	Right Ventricle	heart
25	chr9:100346200-100360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
26	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr9:100349600-100355600	Weak transcription	Left Ventricle	heart
28	chr9:100349800-100356600	Weak transcription	Brain Hippocampus Middle	brain
29	chr9:100350400-100361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
30	chr9:100350600-100353400	Weak transcription	K562	blood
31	chr9:100350600-100360800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr9:100350800-100356600	Weak transcription	Pancreas	Pancrea
33	chr9:100351200-100361800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
34	chr9:100352000-100353600	Weak transcription	Lung	lung
35	chr9:100352000-100353600	Weak transcription	GM12878-XiMat	blood
36	chr9:100353000-100362800	Weak transcription	Esophagus	oesophagus

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links