Variant report

Variant	rs1028178
Chromosome Location	chr2:180350386-180350387
allele	C/T
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:16)

rs_ID	r²[population]
rs13010423	1.00[CHB][hapmap]
rs1517702	1.00[CHB][hapmap]
rs17747577	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs17747835	1.00[CHB][hapmap]
rs17747870	1.00[CHB][hapmap]
rs17748453	1.00[CHB][hapmap]
rs17803813	0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17815250	1.00[CHB][hapmap]
rs1980197	0.84[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177231	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62177235	0.96[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs62177236	0.92[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744352	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.83[GIH][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557169	1.00[CHB][hapmap]
rs9288038	1.00[CHB][hapmap]
rs9973399	1.00[CHB][hapmap]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1028178	HOXD4	cis	cerebellum	SCAN

Chromatin state (count:10 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180309200-180352200	Weak transcription	Skeletal Muscle Male	skeletal muscle
2	chr2:180325200-180351400	Weak transcription	Psoas Muscle	Psoas
3	chr2:180332800-180352600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
4	chr2:180341200-180350600	Strong transcription	Liver	Liver
5	chr2:180348200-180351800	Weak transcription	Skeletal Muscle Female	skeletal muscle
6	chr2:180348400-180351400	Weak transcription	HUVEC	blood vessel
7	chr2:180348600-180352200	Weak transcription	Gastric	stomach
8	chr2:180349600-180353000	Enhancers	Fetal Heart	heart
9	chr2:180350200-180350400	Enhancers	Right Atrium	heart
10	chr2:180350200-180357800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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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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