Variant report

Variant	rs2805792
Chromosome Location	chr9:100353801-100353802
allele	A/C
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: 5 )

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	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2245694	1.00[CEU][hapmap];0.83[GIH][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes]
rs2254733	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2773343	1.00[CEU][hapmap];0.85[CHD][hapmap];1.00[GIH][hapmap];0.82[MEX][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773344	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773349	0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773350	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2773354	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap]
rs2773358	0.96[EUR][1000 genomes]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.86[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805778	1.00[JPT][hapmap]
rs2805783	0.86[CEU][hapmap]
rs2805785	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2805786	0.82[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805787	0.90[EUR][1000 genomes]
rs2805788	0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805793	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805802	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2805804	0.82[EUR][1000 genomes]
rs2805805	0.81[EUR][1000 genomes]
rs2805831	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.84[MEX][hapmap];0.93[TSI][hapmap]
rs2805835	1.00[JPT][hapmap]
rs2808682	1.00[JPT][hapmap]
rs7863516	0.88[ASN][1000 genomes]
rs932916	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2805792	TBC1D2	cis	parietal	SCAN
rs2805792	TMOD1	cis	cerebellum	SCAN
rs2805792	C9orf89	cis	cerebellum	SCAN
rs2805792	ZNF367	cis	parietal	SCAN
rs2805792	TMOD1	cis	multi-tissue	Pritchard

Chromatin state (count:42 , 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	chr9:100334800-100355600	Weak transcription	Rectal Smooth Muscle	rectum
6	chr9:100335600-100356600	Weak transcription	Brain Angular Gyrus	brain
7	chr9:100336200-100356200	Weak transcription	Aorta	Aorta
8	chr9:100336200-100360000	Weak transcription	Brain Substantia Nigra	brain
9	chr9:100338200-100356200	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr9:100338200-100356800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr9:100338400-100356000	Weak transcription	Brain Anterior Caudate	brain
12	chr9:100338400-100361600	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr9:100338600-100360800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
14	chr9:100341200-100358400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
15	chr9:100341600-100356000	Weak transcription	Right Atrium	heart
16	chr9:100342400-100355800	Weak transcription	Right Ventricle	heart
17	chr9:100346200-100360800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
18	chr9:100348800-100384000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr9:100349600-100355600	Weak transcription	Left Ventricle	heart
20	chr9:100349800-100356600	Weak transcription	Brain Hippocampus Middle	brain
21	chr9:100350400-100361800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr9:100350600-100360800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
23	chr9:100350800-100356600	Weak transcription	Pancreas	Pancrea
24	chr9:100351200-100361800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr9:100353000-100362800	Weak transcription	Esophagus	oesophagus
26	chr9:100353200-100354200	Enhancers	Psoas Muscle	Psoas
27	chr9:100353200-100355600	Genic enhancers	Skeletal Muscle Female	skeletal muscle
28	chr9:100353200-100362200	Enhancers	Fetal Brain Male	brain
29	chr9:100353200-100363200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
30	chr9:100353400-100354000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
31	chr9:100353400-100355400	Strong transcription	Stomach Smooth Muscle	stomach
32	chr9:100353400-100359200	Strong transcription	K562	blood
33	chr9:100353600-100354000	Genic enhancers	Lung	lung
34	chr9:100353600-100354200	Genic enhancers	GM12878-XiMat	blood
35	chr9:100353600-100355000	Genic enhancers	Skeletal Muscle Male	skeletal muscle
36	chr9:100353600-100355400	Strong transcription	Colon Smooth Muscle	Colon
37	chr9:100353600-100356200	Enhancers	Fetal Brain Female	brain
38	chr9:100353600-100356200	Strong transcription	Ovary	ovary
39	chr9:100353600-100358600	Enhancers	Fetal Heart	heart
40	chr9:100353800-100354000	Genic enhancers	Fetal Muscle Leg	muscle
41	chr9:100353800-100354600	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr9:100353800-100356200	Weak transcription	Fetal Muscle Trunk	muscle

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