Variant report

Variant	rs17028338
Chromosome Location	chr4:99888786-99888787
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 17 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs17028323	0.91[AFR][1000 genomes]
rs17028328	1.00[ASW][hapmap];0.85[LWK][hapmap];1.00[YRI][hapmap];0.91[AFR][1000 genomes]
rs17028347	0.98[AFR][1000 genomes]
rs2903158	0.89[YRI][hapmap]
rs6833875	1.00[YRI][hapmap]
rs6846054	0.80[AFR][1000 genomes]
rs72906974	0.80[AFR][1000 genomes]
rs72906977	0.80[AFR][1000 genomes]
rs72906984	0.80[AFR][1000 genomes]
rs72906987	0.80[AFR][1000 genomes]
rs72908929	0.87[AFR][1000 genomes]
rs72908930	0.87[AFR][1000 genomes]
rs72908944	0.87[AFR][1000 genomes]
rs72908946	0.87[AFR][1000 genomes]
rs7672509	0.82[ASW][hapmap]
rs7678891	0.87[AFR][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1009017	chr4:99669441-100406394	Active TSS Enhancers Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	57 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17028338	MTTP	cis	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:99885800-99891600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
2	chr4:99886400-99891000	Weak transcription	Osteobl	bone
3	chr4:99886400-99891200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr4:99886400-99891200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr4:99886400-99891200	Weak transcription	NHEK	skin
6	chr4:99886400-99891400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr4:99886600-99891200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
8	chr4:99887400-99888800	Enhancers	Fetal Intestine Small	intestine
9	chr4:99887400-99893600	Weak transcription	HMEC	breast
10	chr4:99887600-99891200	Weak transcription	K562	blood
11	chr4:99888400-99888800	Enhancers	Fetal Intestine Large	intestine

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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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