Variant report

Variant	rs757143
Chromosome Location	chr7:27472307-27472308
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs10268902	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10280925	1.00[ASW][hapmap];0.96[CEU][hapmap];0.80[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.88[AFR][1000 genomes];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1034660	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10951164	0.95[JPT][hapmap];0.82[ASN][1000 genomes]
rs12700805	0.80[JPT][hapmap];0.81[ASN][1000 genomes]
rs17439381	0.86[ASN][1000 genomes]
rs1806799	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1966331	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs34226948	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3846999	0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6651067	0.95[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6951650	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6963552	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][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	nsv830930	chr7:27395838-27587355	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs757143	HOXA7	cis	parietal	SCAN
rs757143	NOD1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27466200-27473800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr7:27469600-27472800	Weak transcription	HUES6 Cell Line	embryonic stem cell
3	chr7:27469800-27473000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr7:27470000-27472800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
5	chr7:27470800-27473200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
6	chr7:27471600-27474200	Enhancers	H1 Cell Line	embryonic stem cell
7	chr7:27472000-27472400	Enhancers	Brain Germinal Matrix	brain
8	chr7:27472000-27473200	Enhancers	HUES48 Cell Line	embryonic stem cell
9	chr7:27472000-27474200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
10	chr7:27472000-27474400	Enhancers	HUES64 Cell Line	embryonic stem cell
11	chr7:27472000-27475200	Enhancers	iPS-15b Cell Line	embryonic stem cell
12	chr7:27472200-27473200	Enhancers	iPS-20b Cell Line	embryonic stem cell
13	chr7:27472200-27473800	Weak transcription	Spleen	Spleen

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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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