Variant report

Variant	rs17747577
Chromosome Location	chr2:180354642-180354643
allele	A/G
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:14)

rs_ID	r²[population]
rs1028178	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs13010423	1.00[CHB][hapmap]
rs1517702	1.00[CHB][hapmap];0.94[YRI][hapmap];0.81[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17747835	1.00[CHB][hapmap]
rs17747870	1.00[CHB][hapmap]
rs17748453	1.00[CHB][hapmap]
rs17803813	1.00[CHB][hapmap]
rs17815250	1.00[CHB][hapmap]
rs62177233	0.99[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6744352	1.00[CHB][hapmap];0.83[CHD][hapmap]
rs72950588	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7557169	0.95[CEU][hapmap];1.00[CHB][hapmap];0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9288038	1.00[CHB][hapmap]
rs9973399	1.00[CHB][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	nsv875468	chr2:180352334-180396869	Enhancers Weak transcription Strong transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases
2	nsv875469	chr2:180354642-180396869	Enhancers Strong transcription Weak transcription Genic enhancers ZNF genes & repeats Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17747577	HOXD4	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:180350200-180357800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
2	chr2:180350400-180355200	Weak transcription	Right Atrium	heart
3	chr2:180350600-180367200	Weak transcription	Liver	Liver
4	chr2:180352400-180360200	Weak transcription	Gastric	stomach
5	chr2:180352600-180360600	Weak transcription	Fetal Intestine Large	intestine
6	chr2:180352800-180378400	Weak transcription	Skeletal Muscle Male	skeletal muscle

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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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