Variant report

Variant	rs12562911
Chromosome Location	chr1:76822600-76822601
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:76816508..76818358-chr1:76820395..76822942,2	K562	blood:

Extended variants
information (count: 55 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:51)

rs_ID	r²[population]
rs1016715	0.82[ASN][1000 genomes]
rs10747346	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10747347	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs10782617	0.84[CHB][hapmap];0.91[YRI][hapmap];0.83[ASN][1000 genomes]
rs10782619	0.82[ASN][1000 genomes]
rs10873881	0.84[ASN][1000 genomes]
rs10873883	0.86[ASN][1000 genomes]
rs11162128	0.84[JPT][hapmap]
rs11162135	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs11162136	0.87[CHB][hapmap];0.82[ASN][1000 genomes]
rs11162137	0.80[ASN][1000 genomes]
rs11162138	0.95[CHB][hapmap];0.88[ASN][1000 genomes]
rs11162139	0.95[CHB][hapmap];0.86[CHD][hapmap];0.86[ASN][1000 genomes]
rs11162141	0.84[ASN][1000 genomes]
rs11162142	0.86[ASN][1000 genomes]
rs11162144	0.91[CHB][hapmap];0.87[YRI][hapmap];0.82[ASN][1000 genomes]
rs11162145	0.82[ASN][1000 genomes]
rs11162146	0.83[ASN][1000 genomes]
rs12021906	0.81[ASN][1000 genomes]
rs12029184	0.83[ASW][hapmap];0.91[CHB][hapmap];0.83[YRI][hapmap];0.81[ASN][1000 genomes]
rs12032409	0.90[CHB][hapmap];0.84[JPT][hapmap];0.92[YRI][hapmap];0.88[ASN][1000 genomes]
rs12034783	1.00[YRI][hapmap];0.88[ASN][1000 genomes]
rs12035993	0.91[CHB][hapmap];0.89[JPT][hapmap];0.89[LWK][hapmap];0.87[MKK][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs12037958	0.83[ASN][1000 genomes]
rs12038570	0.95[CHB][hapmap];0.82[YRI][hapmap];0.88[ASN][1000 genomes]
rs12040892	0.85[CHB][hapmap];0.88[ASN][1000 genomes]
rs12043272	0.83[ASN][1000 genomes]
rs12046895	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs12562224	0.95[CHB][hapmap];0.83[YRI][hapmap];0.86[ASN][1000 genomes]
rs12749057	0.84[ASN][1000 genomes]
rs1325287	0.95[CHB][hapmap];0.86[CHD][hapmap];0.90[JPT][hapmap]
rs1325291	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs1325292	0.81[ASN][1000 genomes]
rs1359467	0.91[CHB][hapmap];0.85[ASN][1000 genomes]
rs1359471	0.91[CHB][hapmap];0.82[ASN][1000 genomes]
rs1408866	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2031482	0.91[CHB][hapmap];0.81[ASN][1000 genomes]
rs2147792	0.95[CHB][hapmap];0.86[ASN][1000 genomes]
rs4426021	0.85[ASN][1000 genomes]
rs4459158	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs4576696	0.85[ASN][1000 genomes]
rs61771501	0.84[ASN][1000 genomes]
rs6664863	0.95[CHB][hapmap];0.86[CHD][hapmap];0.89[ASN][1000 genomes]
rs6666049	0.91[CHB][hapmap];0.83[ASN][1000 genomes]
rs6677296	0.82[CHB][hapmap];0.81[ASN][1000 genomes]
rs6678598	0.95[CHB][hapmap];0.95[JPT][hapmap];0.80[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs6685141	0.84[JPT][hapmap]
rs67776937	0.87[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs7339997	0.90[CHB][hapmap];0.84[ASN][1000 genomes]
rs7340082	0.82[ASN][1000 genomes]
rs9437437	0.85[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	nsv870621	chr1:76620313-76997071	Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
2	nsv534168	chr1:76718950-77039352	Enhancers Active TSS Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
3	nsv1006776	chr1:76777323-76899975	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
4	nsv1014231	chr1:76781140-76880630	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12562911	ST6GALNAC5	cis	cerebellum	SCAN
rs12562911	ELTD1	cis	parietal	SCAN

Chromatin state (count:3 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:76811400-76822800	Weak transcription	Fetal Stomach	stomach
2	chr1:76817800-76829400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr1:76817800-76832200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin

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