Variant report

Variant	rs17161988
Chromosome Location	chr1:223444263-223444264
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	chr1:223407302..223409358-chr1:223443045..223444830,2	K562	blood:
2	chr1:223443250..223444917-chr1:223494926..223496525,2	K562	blood:

Extended variants
information (count: 41 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs1400961	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]
rs1418150	0.83[GIH][hapmap];0.86[TSI][hapmap];0.83[EUR][1000 genomes]
rs1418152	0.85[CEU][hapmap];0.91[TSI][hapmap];0.92[EUR][1000 genomes]
rs1418153	0.93[EUR][1000 genomes]
rs17163765	0.85[CEU][hapmap];0.88[TSI][hapmap];0.91[EUR][1000 genomes]
rs17479856	0.85[CEU][hapmap];0.92[GIH][hapmap];0.93[TSI][hapmap];0.92[EUR][1000 genomes]
rs17517952	0.90[EUR][1000 genomes]
rs17518077	0.90[EUR][1000 genomes]
rs17538964	0.85[CEU][hapmap];0.89[GIH][hapmap];0.93[TSI][hapmap];0.91[EUR][1000 genomes]
rs17576822	0.85[CEU][hapmap];0.86[TSI][hapmap];0.91[EUR][1000 genomes]
rs17577025	0.85[CEU][hapmap];0.88[TSI][hapmap];0.92[EUR][1000 genomes]
rs17577212	0.90[EUR][1000 genomes]
rs1773710	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs1829310	0.90[EUR][1000 genomes]
rs28561511	0.90[EUR][1000 genomes]
rs3820596	1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs61837629	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61837630	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs61837633	0.91[EUR][1000 genomes]
rs61837634	0.93[EUR][1000 genomes]
rs61837635	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs61837636	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs61837638	0.93[EUR][1000 genomes]
rs61837640	0.93[EUR][1000 genomes]
rs61838191	0.92[EUR][1000 genomes]
rs61838192	0.92[EUR][1000 genomes]
rs61838194	0.92[EUR][1000 genomes]
rs61838197	0.90[EUR][1000 genomes]
rs61838199	0.90[EUR][1000 genomes]
rs712857	0.81[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.85[TSI][hapmap];0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs73122234	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7412060	0.92[EUR][1000 genomes]
rs74145795	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7518292	0.92[EUR][1000 genomes]
rs851194	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs851201	0.80[JPT][hapmap]
rs885279	1.00[CEU][hapmap];0.82[MEX][hapmap];0.95[TSI][hapmap];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs9442040	0.90[AMR][1000 genomes];0.86[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9442043	0.93[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
rs17161988	SUSD4	cis	parietal	SCAN
rs17161988	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223433200-223444600	Weak transcription	Esophagus	oesophagus
2	chr1:223440400-223446000	Weak transcription	Brain Anterior Caudate	brain
3	chr1:223440800-223465600	Weak transcription	Ovary	ovary
4	chr1:223441200-223445600	Weak transcription	Pancreatic Islets	Pancreatic Islet
5	chr1:223442200-223445400	Enhancers	Liver	Liver
6	chr1:223442600-223462200	Weak transcription	Primary T cells from cord blood	blood
7	chr1:223443000-223444600	Weak transcription	Pancreas	Pancrea
8	chr1:223443000-223446800	Weak transcription	K562	blood
9	chr1:223443400-223444400	Weak transcription	Fetal Intestine Large	intestine
10	chr1:223443800-223444800	Weak transcription	Stomach Mucosa	stomach
11	chr1:223443800-223472600	Weak transcription	Gastric	stomach
12	chr1:223444200-223444800	Enhancers	Rectal Mucosa Donor 31	rectum

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