Variant report

Variant	rs1396686
Chromosome Location	chr4:126282962-126282963
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 27 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs12511204	1.00[JPT][hapmap]
rs1355161	1.00[CEU][hapmap];0.90[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1533037	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009509	1.00[CEU][hapmap];0.90[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009511	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009520	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.81[MKK][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs17009526	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs17009535	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710544	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2710545	1.00[CEU][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710557	1.00[CEU][hapmap];0.90[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710562	1.00[CEU][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710563	1.00[JPT][hapmap];0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2710591	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2710593	0.99[ASN][1000 genomes]
rs2940780	1.00[CEU][hapmap];0.90[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56995730	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57565770	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs57945315	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs58972262	1.00[EUR][1000 genomes]
rs6830885	1.00[CEU][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs6840704	1.00[EUR][1000 genomes]
rs885271	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs970289	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs972312	1.00[CEU][hapmap];0.90[JPT][hapmap];0.97[AMR][1000 genomes];1.00[EUR][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	nsv1006068	chr4:126103233-126497467	Enhancers ZNF genes & repeats Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	5 gene(s)	inside rSNPs	diseases
2	nsv830051	chr4:126234895-126403426	Enhancers ZNF genes & repeats Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1396686	CD3D	trans	lymphoblastoid	seeQTL

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:126274000-126288800	Weak transcription	Fetal Stomach	stomach
2	chr4:126274000-126289000	Weak transcription	Fetal Brain Male	brain
3	chr4:126274200-126289400	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr4:126276800-126289800	Weak transcription	Fetal Muscle Leg	muscle
5	chr4:126277400-126288800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr4:126280000-126287000	Weak transcription	Fetal Lung	lung
7	chr4:126280000-126288600	Weak transcription	Fetal Kidney	kidney
8	chr4:126281600-126288800	Weak transcription	NHDF-Ad	bronchial
9	chr4:126281800-126283000	Weak transcription	Colon Smooth Muscle	Colon
10	chr4:126281800-126284800	Weak transcription	Cortex derived primary cultured neurospheres	brain
11	chr4:126282000-126288800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
12	chr4:126282000-126288800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
13	chr4:126282000-126289200	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr4:126282600-126293000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr4:126282800-126283000	Enhancers	H9 Cell Line	embryonic stem cell
16	chr4:126282800-126288800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived

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