Variant report

Variant	rs12353519
Chromosome Location	chr9:104339000-104339001
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs10120085	0.84[AFR][1000 genomes]
rs1323419	0.84[CHD][hapmap];0.84[GIH][hapmap];0.96[MEX][hapmap];0.87[TSI][hapmap]
rs13292046	0.83[CEU][hapmap];0.86[CHB][hapmap];0.92[YRI][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs13293899	0.80[AFR][1000 genomes];0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs17188384	0.80[CEU][hapmap];0.85[CHB][hapmap];0.93[YRI][hapmap];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs1983812	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs35168482	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3903803	0.84[CHD][hapmap];0.83[GIH][hapmap]
rs7023854	0.82[CEU][hapmap];0.85[CHB][hapmap];0.95[CHD][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7029878	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs942139	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9886856	0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046975	chr9:104167583-104659873	Weak transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv949579	chr9:104229820-104512923	Genic enhancers Enhancers Strong transcription Active TSS Bivalent/Poised TSS Bivalent Enhancer Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv1052492	chr9:104263419-104387782	Weak transcription Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases
4	nsv831672	chr9:104300755-104480849	Weak transcription Strong transcription Bivalent/Poised TSS Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12353519	TMOD1	cis	cerebellum	SCAN

Chromatin state (count:44 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:104325200-104344400	Weak transcription	NHLF	lung
2	chr9:104325200-104350000	Weak transcription	HSMMtube	muscle
3	chr9:104327000-104344600	Weak transcription	Rectal Smooth Muscle	rectum
4	chr9:104327400-104339600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr9:104327400-104348400	Weak transcription	Aorta	Aorta
6	chr9:104327600-104344400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr9:104327800-104344400	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr9:104328000-104342200	Weak transcription	Colon Smooth Muscle	Colon
9	chr9:104328400-104340600	Weak transcription	GM12878-XiMat	blood
10	chr9:104331800-104344600	Weak transcription	HSMM	muscle
11	chr9:104332400-104344600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr9:104332800-104340600	Weak transcription	Primary B cells from peripheral blood	blood
13	chr9:104333000-104340600	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr9:104333000-104342200	Weak transcription	Spleen	Spleen
15	chr9:104333000-104342400	Weak transcription	Brain Cingulate Gyrus	brain
16	chr9:104333000-104344400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr9:104333000-104344400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
18	chr9:104333000-104344800	Weak transcription	A549	lung
19	chr9:104333400-104340000	Weak transcription	Monocytes-CD14+_RO01746	blood
20	chr9:104333400-104340600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr9:104333400-104340800	Weak transcription	Primary B cells from cord blood	blood
22	chr9:104333400-104342400	Weak transcription	Fetal Stomach	stomach
23	chr9:104335200-104340600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
24	chr9:104335200-104344600	Weak transcription	HUES64 Cell Line	embryonic stem cell
25	chr9:104335400-104340600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr9:104335400-104344600	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr9:104335400-104344800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
28	chr9:104335600-104340400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
29	chr9:104335600-104340600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr9:104335600-104340800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
31	chr9:104335600-104344400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
32	chr9:104335600-104344600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr9:104335600-104346000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr9:104335800-104340800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
35	chr9:104335800-104340800	Weak transcription	HUES6 Cell Line	embryonic stem cell
36	chr9:104336000-104340600	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr9:104336600-104340600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr9:104337800-104339200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
39	chr9:104337800-104339800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
40	chr9:104337800-104340600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr9:104337800-104340600	Weak transcription	Fetal Brain Male	brain
42	chr9:104338200-104344400	Weak transcription	Fetal Brain Female	brain
43	chr9:104338800-104340400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
44	chr9:104338800-104340600	Weak transcription	Muscle Satellite Cultured Cells	--

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