Variant report

Variant	rs969410
Chromosome Location	chr7:27474713-27474714
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr7:27462153..27463834-chr7:27472462..27475213,2	MCF-7	breast:
2	chr7:27468218..27471547-chr7:27472130..27475962,5	K562	blood:
3	chr7:27470047..27472027-chr7:27474314..27477072,2	K562	blood:

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11563953	0.93[CEU][hapmap];0.91[GIH][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs11981704	0.81[TSI][hapmap]
rs11981761	0.81[TSI][hapmap]
rs12700804	0.90[EUR][1000 genomes]
rs12700806	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1541359	0.92[EUR][1000 genomes]
rs1554637	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs17429761	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs34600677	1.00[ASN][1000 genomes]
rs34924985	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34989520	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35240477	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35468459	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs35713538	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3915087	0.91[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3915088	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4722704	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6958811	0.85[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs6970308	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs6979081	0.93[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs71539516	0.81[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7784592	1.00[CEU][hapmap];0.92[MEX][hapmap];0.97[TSI][hapmap];0.93[YRI][hapmap];0.94[EUR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs969410	HOXA3	cis	cerebellum	SCAN

Chromatin state (count:15 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:27472000-27475200	Enhancers	iPS-15b Cell Line	embryonic stem cell
2	chr7:27472800-27474800	Enhancers	HUES6 Cell Line	embryonic stem cell
3	chr7:27472800-27475200	Enhancers	iPS-18 Cell Line	embryonic stem cell
4	chr7:27473000-27475200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr7:27473600-27474800	Weak transcription	Brain Germinal Matrix	brain
6	chr7:27474000-27475200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
7	chr7:27474000-27475200	Enhancers	Rectal Mucosa Donor 31	rectum
8	chr7:27474000-27475800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
9	chr7:27474000-27476400	Weak transcription	Spleen	Spleen
10	chr7:27474200-27475800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
11	chr7:27474400-27475200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
12	chr7:27474400-27475400	Enhancers	Fetal Stomach	stomach
13	chr7:27474400-27475800	Enhancers	Osteobl	bone
14	chr7:27474600-27475200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr7:27474600-27475600	Enhancers	Muscle Satellite Cultured Cells	--

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