Variant report

Variant	rs17539583
Chromosome Location	chr1:223520861-223520862
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	chr1:223514593..223516719-chr1:223519953..223521559,2	K562	blood:
2	chr1:223519202..223521587-chr1:223525632..223530010,3	MCF-7	breast:

Extended variants
information (count: 63 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10495206	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10495207	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10907376	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11261264	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11261270	0.80[ASN][1000 genomes]
rs12123148	0.83[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12140453	0.89[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12564615	0.89[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1400959	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.81[TSI][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs1547788	0.82[EUR][1000 genomes]
rs17162008	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17162072	0.92[JPT][hapmap]
rs17163824	0.84[EUR][1000 genomes]
rs17163825	0.83[EUR][1000 genomes]
rs17163827	0.91[EUR][1000 genomes]
rs17163828	0.85[EUR][1000 genomes]
rs17163831	0.83[EUR][1000 genomes]
rs17479856	0.83[JPT][hapmap]
rs17480087	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17480344	1.00[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs17518349	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17518363	0.86[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.82[CHD][hapmap];0.92[JPT][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17538964	0.83[JPT][hapmap]
rs17539269	0.84[ASW][hapmap];0.94[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];0.85[MKK][hapmap];0.94[TSI][hapmap];0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17577742	0.84[ASW][hapmap];0.83[CEU][hapmap];0.85[MEX][hapmap];0.82[TSI][hapmap];0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17578168	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17578203	0.84[ASW][hapmap];0.89[CEU][hapmap];1.00[CHB][hapmap];0.88[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];0.86[TSI][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1772280	0.83[EUR][1000 genomes]
rs2138966	0.81[ASN][1000 genomes]
rs34150324	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35318812	0.84[EUR][1000 genomes]
rs59355120	0.81[ASN][1000 genomes]
rs61838208	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61838209	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs61838210	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61838229	0.94[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61838230	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61838231	1.00[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs61838234	0.82[EUR][1000 genomes]
rs61838235	0.82[EUR][1000 genomes]
rs61838236	0.84[EUR][1000 genomes]
rs61838237	0.84[EUR][1000 genomes]
rs61838238	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838239	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838240	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61838241	0.84[EUR][1000 genomes]
rs61838243	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs61838246	0.83[EUR][1000 genomes]
rs61838249	0.84[EUR][1000 genomes]
rs61838250	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838252	0.83[EUR][1000 genomes]
rs61839867	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs61839876	0.81[ASN][1000 genomes]
rs61839877	0.81[ASN][1000 genomes]
rs61839878	0.81[ASN][1000 genomes]
rs61839879	0.81[ASN][1000 genomes]
rs7536652	0.82[EUR][1000 genomes]
rs7541162	0.81[EUR][1000 genomes]
rs870486	0.84[EUR][1000 genomes]
rs9442042	0.94[AFR][1000 genomes];0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9442046	0.81[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	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
2	nsv1010798	chr1:223498145-223538989	Enhancers Flanking Bivalent TSS/Enh Weak transcription Bivalent Enhancer Flanking Active TSS Bivalent/Poised TSS Active TSS Strong transcription	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17539583	SUSD4	cis	cerebellum	SCAN
rs17539583	SUSD4	cis	Heart Left Ventricle	GTEx
rs17539583	SUSD4	cis	parietal	SCAN

Chromatin state (count:9 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223505600-223521400	Weak transcription	Primary T cells from cord blood	blood
2	chr1:223506600-223526000	Weak transcription	Esophagus	oesophagus
3	chr1:223511800-223527000	Enhancers	Fetal Heart	heart
4	chr1:223514000-223526200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
5	chr1:223514400-223535800	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr1:223515400-223523200	Weak transcription	Fetal Muscle Leg	muscle
7	chr1:223515600-223523400	Weak transcription	Gastric	stomach
8	chr1:223517600-223527400	Enhancers	Ovary	ovary
9	chr1:223520800-223521400	Enhancers	Stomach Mucosa	stomach

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