Variant report

Variant	rs1536950
Chromosome Location	chr9:100333772-100333773
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr9:100333571..100335590-chr9:100340872..100342993,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10123528	1.00[JPT][hapmap]
rs10982745	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[MEX][hapmap];0.83[AMR][1000 genomes]
rs16922598	1.00[JPT][hapmap]
rs2773343	0.85[CHD][hapmap]
rs2773344	1.00[JPT][hapmap];0.81[YRI][hapmap]
rs2773350	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2773354	1.00[JPT][hapmap]
rs2805768	1.00[JPT][hapmap]
rs2805771	1.00[JPT][hapmap]
rs2805773	1.00[JPT][hapmap]
rs2805774	0.85[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap]
rs2805778	1.00[JPT][hapmap]
rs2805802	0.89[ASN][1000 genomes]
rs2805804	0.89[ASN][1000 genomes]
rs2805805	0.82[AFR][1000 genomes];0.89[ASN][1000 genomes]
rs2805808	0.95[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2805810	0.86[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2805831	0.85[CHD][hapmap];1.00[JPT][hapmap]
rs2805835	1.00[JPT][hapmap]
rs2808682	1.00[JPT][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs1536950	TMOD1	cis	cerebellum	SCAN
rs1536950	GALNT12	cis	parietal	SCAN
rs1536950	C9orf3	cis	cerebellum	SCAN
rs1536950	C9orf130	cis	parietal	SCAN

Chromatin state (count:46 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:100326800-100337000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr9:100327000-100349200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr9:100327200-100340000	Weak transcription	Fetal Stomach	stomach
4	chr9:100327400-100335400	Weak transcription	Hela-S3	cervix
5	chr9:100330400-100339400	Weak transcription	Brain Germinal Matrix	brain
6	chr9:100330800-100336200	Strong transcription	K562	blood
7	chr9:100331000-100334600	Strong transcription	Lung	lung
8	chr9:100331200-100334200	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
9	chr9:100331200-100335200	Genic enhancers	Fetal Muscle Leg	muscle
10	chr9:100332000-100333800	Genic enhancers	Colon Smooth Muscle	Colon
11	chr9:100332000-100335000	Genic enhancers	Fetal Heart	heart
12	chr9:100332400-100334400	Enhancers	Brain Substantia Nigra	brain
13	chr9:100332400-100334400	Genic enhancers	Stomach Smooth Muscle	stomach
14	chr9:100332400-100334800	Genic enhancers	Skeletal Muscle Male	skeletal muscle
15	chr9:100332400-100335000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr9:100332600-100334200	Enhancers	Psoas Muscle	Psoas
17	chr9:100332600-100334400	Genic enhancers	Brain Dorsolateral Prefrontal Cortex	brain
18	chr9:100332600-100334400	Enhancers	HSMMtube	muscle
19	chr9:100332600-100334600	Genic enhancers	Brain Anterior Caudate	brain
20	chr9:100332600-100335600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr9:100332600-100336400	Strong transcription	Pancreatic Islets	Pancreatic Islet
22	chr9:100332800-100334000	Enhancers	Adipose Nuclei	Adipose
23	chr9:100332800-100334400	Genic enhancers	Brain Angular Gyrus	brain
24	chr9:100332800-100334400	Enhancers	Brain Cingulate Gyrus	brain
25	chr9:100332800-100334600	Strong transcription	GM12878-XiMat	blood
26	chr9:100332800-100334800	Enhancers	Rectal Smooth Muscle	rectum
27	chr9:100332800-100335000	Enhancers	Fetal Muscle Trunk	muscle
28	chr9:100333000-100334200	Enhancers	Cortex derived primary cultured neurospheres	brain
29	chr9:100333000-100334200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr9:100333000-100335600	Enhancers	Liver	Liver
31	chr9:100333200-100334000	Enhancers	Right Atrium	heart
32	chr9:100333200-100334200	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr9:100333200-100334400	Enhancers	Brain Inferior Temporal Lobe	brain
34	chr9:100333200-100334800	Enhancers	Left Ventricle	heart
35	chr9:100333400-100334000	Weak transcription	Spleen	Spleen
36	chr9:100333400-100334600	Weak transcription	Fetal Brain Female	brain
37	chr9:100333400-100338400	Strong transcription	Ovary	ovary
38	chr9:100333400-100340800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
39	chr9:100333600-100334000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr9:100333600-100334600	Enhancers	Brain Hippocampus Middle	brain
41	chr9:100333600-100335200	Enhancers	Skeletal Muscle Female	skeletal muscle
42	chr9:100333600-100335400	Genic enhancers	Right Ventricle	heart
43	chr9:100333600-100336200	Strong transcription	Aorta	Aorta
44	chr9:100333600-100339400	Weak transcription	Pancreas	Pancrea
45	chr9:100333600-100341400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr9:100333600-100361800	Weak transcription	Gastric	stomach

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