Variant report

Variant	rs627406
Chromosome Location	chr1:168674954-168674955
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:168674549..168676418-chr1:169074810..169077657,3	MCF-7	breast:
2	chr1:168674465..168676226-chr1:168704172..168705737,2	K562	blood:

Variant related genes	Relation type
ENSG00000143153	Chromatin interaction

Extended variants
information (count: 28 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:24)

rs_ID	r²[population]
rs494317	0.83[ASN][1000 genomes]
rs512129	0.86[JPT][hapmap]
rs520084	0.81[ASN][1000 genomes]
rs524705	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.91[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs528953	0.86[JPT][hapmap]
rs530022	0.87[CHB][hapmap];0.82[JPT][hapmap];0.83[ASN][1000 genomes]
rs542149	0.81[JPT][hapmap]
rs545833	0.86[JPT][hapmap]
rs580360	0.87[CHB][hapmap];0.82[JPT][hapmap]
rs581753	0.81[JPT][hapmap]
rs586318	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs597584	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs598416	0.82[CHB][hapmap];0.82[JPT][hapmap];0.81[ASN][1000 genomes]
rs59849641	0.82[ASN][1000 genomes]
rs603259	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs607484	0.86[JPT][hapmap]
rs612680	0.91[ASN][1000 genomes]
rs627098	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs630159	0.82[CHB][hapmap];0.82[JPT][hapmap];0.80[MEX][hapmap];0.83[ASN][1000 genomes]
rs631451	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs656529	0.86[ASN][1000 genomes]
rs680531	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs681445	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs686226	0.81[JPT][hapmap]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007846	chr1:168449940-168687265	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv869415	chr1:168467284-169153863	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	44 gene(s)	inside rSNPs	diseases
3	nsv831836	chr1:168538779-168716956	Enhancers Flanking Active TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
4	nsv831847	chr1:168669877-168850129	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs627406	ALDH9A1	cis	parietal	SCAN

Chromatin state (count:7 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:168665600-168677600	Weak transcription	Fetal Heart	heart
2	chr1:168666000-168679000	Weak transcription	Duodenum Smooth Muscle	Duodenum
3	chr1:168666200-168675600	Weak transcription	Fetal Stomach	stomach
4	chr1:168670000-168675800	Weak transcription	Adipose Nuclei	Adipose
5	chr1:168670600-168677800	Weak transcription	Small Intestine	intestine
6	chr1:168671400-168677600	Weak transcription	Fetal Intestine Large	intestine
7	chr1:168673800-168678800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived

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