Variant report

Variant	rs626376
Chromosome Location	chr1:84516043-84516044
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:84515190..84517358-chr1:84542033..84543983,2	K562	blood:
2	chr1:84506312..84509081-chr1:84514938..84517601,2	MCF-7	breast:
3	chr1:84507131..84508951-chr1:84514289..84516421,2	K562	blood:

Variant related genes	Relation type
ENSG00000271576	Chromatin interaction
ENSG00000142875	Chromatin interaction

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs1016379	0.87[ASW][hapmap];0.82[CHD][hapmap]
rs12035258	0.85[YRI][hapmap]
rs1811643	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2139931	0.82[CHD][hapmap]
rs2182199	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2642184	0.87[ASW][hapmap];0.86[CHD][hapmap];0.85[YRI][hapmap]
rs2684914	0.87[ASW][hapmap]
rs2812451	0.83[CHB][hapmap];0.82[YRI][hapmap]
rs2892811	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs471151	0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs481354	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs484505	0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs512737	1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.88[EUR][1000 genomes]
rs522892	0.87[EUR][1000 genomes]
rs523531	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532246	0.86[CEU][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.88[EUR][1000 genomes]
rs562971	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs566830	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs575577	0.85[EUR][1000 genomes]
rs592905	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs593763	0.88[EUR][1000 genomes]
rs593869	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs597594	0.85[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap]
rs602568	0.83[EUR][1000 genomes]
rs603447	0.87[EUR][1000 genomes]
rs615352	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs618232	0.86[CEU][hapmap];1.00[JPT][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.83[EUR][1000 genomes]
rs625107	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs629277	0.93[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs649226	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[EUR][1000 genomes]
rs6576955	0.83[EUR][1000 genomes]
rs659227	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs659743	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs663521	0.84[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs664508	0.87[EUR][1000 genomes]
rs6666984	0.83[EUR][1000 genomes]
rs667304	1.00[CHB][hapmap];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs669110	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs671209	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs671561	0.85[EUR][1000 genomes]
rs678794	0.86[CEU][hapmap];1.00[CHB][hapmap];0.90[CHD][hapmap];0.85[GIH][hapmap];1.00[JPT][hapmap];1.00[TSI][hapmap];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs680627	1.00[JPT][hapmap];0.83[EUR][1000 genomes]
rs680905	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.86[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs683074	0.86[CEU][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];0.95[MKK][hapmap];1.00[TSI][hapmap];0.87[EUR][1000 genomes]
rs684114	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs684651	0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs726607	0.81[CEU][hapmap];0.93[MKK][hapmap];1.00[TSI][hapmap];0.82[EUR][1000 genomes]
rs810915	0.86[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.96[TSI][hapmap];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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	nsv1732	chr1:84499098-84544635	Flanking Active TSS Enhancers Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv508360	chr1:84500230-84524997	Bivalent Enhancer Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS	Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
3	esv3498832	chr1:84514725-84525109	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases
4	esv3498833	chr1:84514725-84525109	Enhancers	Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs626376	LPHN2	cis	parietal	SCAN

Chromatin state (count:0 , 50 per page) page:

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dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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