Variant report

Variant	rs4147268
Chromosome Location	chr1:217084292-217084293
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 12 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs1025651	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1025654	0.94[CEU][hapmap]
rs1469891	0.96[YRI][hapmap];0.83[AFR][1000 genomes]
rs2576202	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2576270	0.95[CEU][hapmap];1.00[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818742	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818743	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2818744	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4436447	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.90[TSI][hapmap];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6688971	0.82[CEU][hapmap];0.89[JPT][hapmap]

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	nsv873179	chr1:217056893-217112871	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv873180	chr1:217073060-217112871	Enhancers Weak transcription Flanking Active TSS Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs4147268	ATF3	cis	cerebellum	SCAN
rs4147268	LZIC	trans	lymphoblastoid	seeQTL

Chromatin state (count:11 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:217062800-217087800	Weak transcription	Fetal Muscle Leg	muscle
2	chr1:217078600-217088000	Weak transcription	Right Atrium	heart
3	chr1:217079000-217086400	Weak transcription	Fetal Heart	heart
4	chr1:217082000-217095000	Weak transcription	Fetal Intestine Small	intestine
5	chr1:217082800-217084400	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr1:217083000-217085000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr1:217083200-217085000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr1:217083200-217088000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
9	chr1:217083800-217085400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr1:217084000-217084800	Enhancers	Brain Substantia Nigra	brain
11	chr1:217084200-217088400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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