Variant report

Variant	rs17163762
Chromosome Location	chr1:223445262-223445263
allele	A/C
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: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs1095170	0.91[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1341289	0.82[YRI][hapmap]
rs1341291	1.00[ASW][hapmap];1.00[CEU][hapmap];0.89[GIH][hapmap];0.87[MEX][hapmap];0.90[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1356481	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1356482	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs1400961	0.86[YRI][hapmap];0.81[AFR][1000 genomes]
rs17161989	0.86[YRI][hapmap]
rs17161993	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17161994	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.98[TSI][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17163767	0.86[YRI][hapmap]
rs17163773	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.89[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs17163774	1.00[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.95[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.92[MEX][hapmap];0.85[MKK][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.87[AFR][1000 genomes];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs17487717	0.93[YRI][hapmap]
rs17518279	0.84[CEU][hapmap];0.93[GIH][hapmap];0.84[MEX][hapmap];0.91[TSI][hapmap];0.89[EUR][1000 genomes]
rs1949441	0.93[YRI][hapmap]
rs2176505	0.89[YRI][hapmap]
rs2203763	1.00[ASW][hapmap];0.95[CEU][hapmap];0.87[GIH][hapmap];0.96[MEX][hapmap];0.93[TSI][hapmap];1.00[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2678367	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2795063	1.00[CEU][hapmap];0.87[GIH][hapmap];0.83[MEX][hapmap];0.93[TSI][hapmap];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs34013846	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs34283624	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs34468460	0.89[YRI][hapmap]
rs34782082	0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34788475	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs35133329	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35345711	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4661252	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61837635	0.81[AFR][1000 genomes]
rs6662301	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs73122234	0.81[AFR][1000 genomes]
rs7536652	0.82[YRI][hapmap]
rs885279	0.92[LWK][hapmap];0.93[YRI][hapmap];0.89[AFR][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs17163762	SUSD4	cis	parietal	SCAN

Chromatin state (count:8 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223440400-223446000	Weak transcription	Brain Anterior Caudate	brain
2	chr1:223440800-223465600	Weak transcription	Ovary	ovary
3	chr1:223441200-223445600	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:223442200-223445400	Enhancers	Liver	Liver
5	chr1:223442600-223462200	Weak transcription	Primary T cells from cord blood	blood
6	chr1:223443000-223446800	Weak transcription	K562	blood
7	chr1:223443800-223472600	Weak transcription	Gastric	stomach
8	chr1:223444800-223445800	Enhancers	Stomach Mucosa	stomach

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