Variant report

Variant	rs1327873
Chromosome Location	chr1:70866249-70866250
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:70812176..70814908-chr1:70864607..70866509,2	K562	blood:
2	chr1:70862085..70864122-chr1:70865724..70868796,3	K562	blood:
3	chr1:70860587..70864293-chr1:70864361..70869013,4	K562	blood:
4	chr1:70819028..70821982-chr1:70865141..70867182,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000118454	Chromatin interaction
ENSG00000197568	Chromatin interaction

Extended variants
information (count: 43 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10465863	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs11209599	0.91[CEU][hapmap]
rs11209600	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.89[AMR][1000 genomes]
rs11209602	0.87[AMR][1000 genomes]
rs11209603	0.83[AMR][1000 genomes]
rs11209608	0.86[AMR][1000 genomes]
rs11209611	0.88[YRI][hapmap];0.91[AMR][1000 genomes]
rs12028257	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs12030275	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12031053	0.91[CEU][hapmap];0.89[AMR][1000 genomes]
rs12034101	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12036256	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.82[AMR][1000 genomes]
rs12037272	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes]
rs12042565	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12565458	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12565460	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs17131276	0.91[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17131285	0.91[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1969953	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs4560989	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes]
rs4650038	0.91[CEU][hapmap];0.86[AMR][1000 genomes]
rs4650041	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes]
rs4650047	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];1.00[GIH][hapmap];0.94[JPT][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56211824	0.89[AMR][1000 genomes]
rs58997663	0.86[AMR][1000 genomes]
rs59821213	0.89[AMR][1000 genomes]
rs60602940	0.82[AMR][1000 genomes]
rs61122312	0.88[AMR][1000 genomes]
rs61587863	0.86[AMR][1000 genomes]
rs61678482	0.89[AMR][1000 genomes]
rs6686181	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.88[AMR][1000 genomes]
rs72678630	0.89[AMR][1000 genomes]
rs72678644	0.89[AMR][1000 genomes]
rs72678645	0.89[AMR][1000 genomes]
rs72678646	0.91[AMR][1000 genomes]
rs72680732	0.92[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7539544	0.91[CEU][hapmap];0.93[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs768433	0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];0.91[TSI][hapmap];0.86[AMR][1000 genomes]
rs998523	1.00[ASW][hapmap];0.91[CEU][hapmap];0.97[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][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	nsv999219	chr1:70730556-71014911	Enhancers Weak transcription Flanking Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	49 gene(s)	inside rSNPs	diseases
2	nsv830137	chr1:70765921-70958718	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	48 gene(s)	inside rSNPs	diseases
3	esv1797324	chr1:70858435-70876569	Flanking Active TSS Enhancers Active TSS Weak transcription Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	13 gene(s)	inside rSNPs	n/a
4	nsv871100	chr1:70859397-70928786	Weak transcription Strong transcription Flanking Active TSS Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1327873	HHLA3	Cis_1M	lymphoblastoid	RTeQTL
rs1327873	SFRS11	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:5 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:70865200-70866600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr1:70865600-70866600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr1:70865800-70866800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr1:70866000-70866600	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr1:70866200-70866600	Enhancers	Brain Inferior Temporal Lobe	brain

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