Variant report

Variant	rs1400961
Chromosome Location	chr1:223446246-223446247
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	chr1:223431564..223434363-chr1:223444284..223446683,2	MCF-7	breast:

Extended variants
information (count: 52 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:50)

rs_ID	r²[population]
rs1341291	0.86[YRI][hapmap]
rs1418150	0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1418152	0.85[CEU][hapmap];0.90[GIH][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1418153	0.92[EUR][1000 genomes]
rs1640849	0.88[ASW][hapmap];0.82[TSI][hapmap];0.80[EUR][1000 genomes]
rs17161988	1.00[CEU][hapmap];0.85[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs17161989	0.91[LWK][hapmap];1.00[YRI][hapmap]
rs17163762	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs17163765	0.88[ASW][hapmap];0.85[CEU][hapmap];0.92[GIH][hapmap];0.81[MEX][hapmap];0.93[TSI][hapmap];0.93[EUR][1000 genomes]
rs17163767	0.88[LWK][hapmap];0.91[MKK][hapmap];1.00[YRI][hapmap]
rs17163773	0.86[YRI][hapmap]
rs17163774	0.86[YRI][hapmap]
rs17163825	0.81[JPT][hapmap]
rs17479856	0.85[CEU][hapmap];0.89[TSI][hapmap];0.91[EUR][1000 genomes]
rs17517952	0.89[EUR][1000 genomes]
rs17518077	0.89[EUR][1000 genomes]
rs17538964	0.85[CEU][hapmap];0.80[GIH][hapmap];0.89[TSI][hapmap];0.90[EUR][1000 genomes]
rs17576822	0.85[CEU][hapmap];0.84[GIH][hapmap];0.81[MEX][hapmap];0.91[TSI][hapmap];0.93[EUR][1000 genomes]
rs17577025	0.85[CEU][hapmap];0.90[GIH][hapmap];0.89[TSI][hapmap];0.92[EUR][1000 genomes]
rs17577212	0.89[EUR][1000 genomes]
rs1773710	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1829310	0.89[EUR][1000 genomes]
rs2203763	0.86[YRI][hapmap]
rs28561511	0.89[EUR][1000 genomes]
rs3820596	0.82[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.97[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61837629	0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61837630	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs61837633	0.93[EUR][1000 genomes]
rs61837634	0.92[EUR][1000 genomes]
rs61837635	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837636	0.91[AFR][1000 genomes];0.88[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61837638	0.92[EUR][1000 genomes]
rs61837640	0.92[EUR][1000 genomes]
rs61838191	0.91[EUR][1000 genomes]
rs61838192	0.91[EUR][1000 genomes]
rs61838194	0.91[EUR][1000 genomes]
rs61838197	0.89[EUR][1000 genomes]
rs61838199	0.89[EUR][1000 genomes]
rs712857	0.82[ASW][hapmap];0.81[CEU][hapmap];0.89[TSI][hapmap];0.88[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs73122234	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs7412060	0.91[EUR][1000 genomes]
rs74145795	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7518292	0.91[EUR][1000 genomes]
rs7536652	0.90[JPT][hapmap]
rs851194	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs851196	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs851201	0.85[CHD][hapmap];0.95[JPT][hapmap];0.81[MEX][hapmap]
rs885279	0.94[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.97[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];1.00[TSI][hapmap];0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9442040	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs9442043	0.92[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1012537	chr1:222755091-223512243	Weak transcription Strong transcription Enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
2	nsv1000039	chr1:223429733-223527845	Enhancers Weak transcription Strong transcription Bivalent Enhancer Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs1400961	SUSD4	cis	parietal	SCAN
rs1400961	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:6 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223440800-223465600	Weak transcription	Ovary	ovary
2	chr1:223442600-223462200	Weak transcription	Primary T cells from cord blood	blood
3	chr1:223443000-223446800	Weak transcription	K562	blood
4	chr1:223443800-223472600	Weak transcription	Gastric	stomach
5	chr1:223446000-223446400	Enhancers	Brain Anterior Caudate	brain
6	chr1:223446200-223449600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast

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