Variant report

Variant	rs1364407
Chromosome Location	chr7:136609925-136609926
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 32 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10242108	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs10243944	0.95[YRI][hapmap];0.81[AFR][1000 genomes]
rs10488600	0.90[CHD][hapmap]
rs1158586	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs12155015	0.96[CEU][hapmap];0.83[MEX][hapmap];0.92[TSI][hapmap]
rs1364408	0.82[CHB][hapmap]
rs1364409	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1378645	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1378646	0.96[CEU][hapmap];0.83[CHB][hapmap];0.81[CHD][hapmap];0.85[GIH][hapmap];0.87[MEX][hapmap];0.97[TSI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1378647	0.96[CEU][hapmap];0.87[CHB][hapmap];0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs1424386	0.87[CHB][hapmap];0.86[JPT][hapmap]
rs1455857	0.91[CEU][hapmap];0.87[MEX][hapmap];0.89[MKK][hapmap];0.90[TSI][hapmap];0.92[AMR][1000 genomes]
rs1455858	0.91[CEU][hapmap];0.87[CHB][hapmap];0.82[CHD][hapmap];0.96[MEX][hapmap];0.93[MKK][hapmap];0.92[TSI][hapmap];0.92[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17168819	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs1824024	0.91[CEU][hapmap];0.87[AMR][1000 genomes]
rs2350780	0.87[CHB][hapmap];0.95[JPT][hapmap];0.87[MEX][hapmap];0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2350783	0.96[CEU][hapmap];0.87[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6467695	0.96[CEU][hapmap];0.87[CHB][hapmap];0.81[JPT][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs6467696	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6942627	0.83[AMR][1000 genomes]
rs6943950	0.81[AMR][1000 genomes]
rs6945230	0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs6947206	0.92[LWK][hapmap];0.85[MKK][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes]
rs6952264	0.96[CEU][hapmap];0.83[AMR][1000 genomes]
rs6960707	0.96[CEU][hapmap];0.83[GIH][hapmap];0.87[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6963819	0.87[CHB][hapmap];0.95[JPT][hapmap]
rs7782965	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7792449	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7806357	0.82[CHB][hapmap];0.93[CHD][hapmap]
rs978437	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1029192	chr7:136433278-137147566	Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831147	chr7:136583444-136755741	Enhancers Weak transcription ZNF genes & repeats Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	8 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1364407	TRIM24	cis	parietal	SCAN
rs1364407	PLXNA4	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:136605200-136612200	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
2	chr7:136605400-136610600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
3	chr7:136607000-136610600	Weak transcription	Right Ventricle	heart
4	chr7:136607000-136612200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
5	chr7:136607800-136611200	Weak transcription	Rectal Smooth Muscle	rectum
6	chr7:136607800-136638000	Weak transcription	NHLF	lung
7	chr7:136608400-136610400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr7:136608600-136610400	Weak transcription	Stomach Smooth Muscle	stomach
9	chr7:136608600-136610800	Enhancers	Primary hematopoietic stem cells	blood
10	chr7:136609000-136612000	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr7:136609400-136610000	Enhancers	Hela-S3	cervix
12	chr7:136609400-136610400	Enhancers	NH-A	brain
13	chr7:136609400-136610800	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
14	chr7:136609400-136610800	Enhancers	Colon Smooth Muscle	Colon
15	chr7:136609400-136610800	Enhancers	Fetal Stomach	stomach
16	chr7:136609600-136610400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
17	chr7:136609600-136610400	Flanking Active TSS	HUVEC	blood vessel
18	chr7:136609600-136610600	Weak transcription	Fetal Lung	lung
19	chr7:136609600-136610600	Weak transcription	Left Ventricle	heart
20	chr7:136609600-136610600	Enhancers	Osteobl	bone
21	chr7:136609600-136610800	Enhancers	Duodenum Smooth Muscle	Duodenum
22	chr7:136609600-136613600	Weak transcription	H9 Cell Line	embryonic stem cell
23	chr7:136609800-136610000	Flanking Active TSS	Fetal Heart	heart

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