Variant report

Variant	rs1570699
Chromosome Location	chr1:158145229-158145230
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:158137977..158140665-chr1:158145143..158147474,2	MCF-7	breast:
2	chr1:158143331..158145618-chr1:158149184..158151309,2	K562	blood:

Variant related genes	Relation type
ENSG00000158473	Chromatin interaction

Extended variants
information (count: 59 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs10489821	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10489823	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040592	0.91[CEU][hapmap]
rs12723141	0.95[JPT][hapmap]
rs1633141	0.92[CEU][hapmap]
rs1633149	0.92[CEU][hapmap]
rs16839951	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1748383	0.92[CEU][hapmap]
rs1748387	0.92[CEU][hapmap]
rs1980757	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2518477	0.92[CEU][hapmap]
rs3021476	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3021478	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3087210	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087211	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087212	1.00[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3087213	0.84[EUR][1000 genomes]
rs3118165	0.92[CEU][hapmap]
rs368130	0.92[CEU][hapmap]
rs374513	0.92[CEU][hapmap]
rs377795	0.92[CEU][hapmap]
rs383688	0.92[CEU][hapmap]
rs384414	0.92[CEU][hapmap]
rs389495	0.91[CEU][hapmap]
rs393304	0.84[CEU][hapmap]
rs401904	0.92[CEU][hapmap]
rs402699	0.92[CEU][hapmap]
rs407309	0.92[CEU][hapmap]
rs413557	0.92[CEU][hapmap]
rs434570	0.92[CEU][hapmap]
rs440862	0.92[CEU][hapmap]
rs448005	0.92[CEU][hapmap]
rs448556	0.92[CEU][hapmap]
rs449838	0.92[CEU][hapmap]
rs594364	0.92[CEU][hapmap]
rs607948	0.92[CEU][hapmap]
rs623215	0.92[CEU][hapmap]
rs6692064	0.88[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6692133	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs691077	0.81[CEU][hapmap]
rs691175	0.92[CEU][hapmap]
rs691551	0.92[CEU][hapmap]
rs72711995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72711999	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7530662	0.92[CEU][hapmap];0.90[JPT][hapmap];0.88[MEX][hapmap]
rs7548147	1.00[JPT][hapmap]
rs7556487	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859001	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859002	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859003	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859005	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs859008	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs859009	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859010	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.95[JPT][hapmap];0.94[TSI][hapmap];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs859011	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs859013	1.00[CEU][hapmap];0.86[CHB][hapmap];0.98[CHD][hapmap];0.92[GIH][hapmap];1.00[JPT][hapmap];0.94[TSI][hapmap];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv999542	chr1:158015715-158368132	Bivalent Enhancer Genic enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
2	nsv872479	chr1:158118787-158484285	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Strong transcription Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	18 gene(s)	inside rSNPs	diseases
3	nsv946435	chr1:158144162-158145633	Weak transcription Enhancers	TF binding region Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs1570699	SHE	cis	cerebellum	SCAN
rs1570699	CD1A	cis	cerebellum	SCAN
rs1570699	NCSTN	cis	cerebellum	SCAN
rs1570699	LCE1E	cis	parietal	SCAN
rs1570699	IQGAP3	cis	cerebellum	SCAN
rs1570699	VHLL	cis	parietal	SCAN

Chromatin state (count:2 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:158139400-158147400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:158143800-158149000	Weak transcription	Small Intestine	intestine

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