Variant report

Variant	rs1400963
Chromosome Location	chr1:223478816-223478817
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	chr1:223472503..223474796-chr1:223478639..223480943,2	K562	blood:

Extended variants
information (count: 35 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10495206	0.82[JPT][hapmap]
rs1341988	0.82[JPT][hapmap]
rs1400959	0.82[JPT][hapmap]
rs1418150	0.91[ASW][hapmap];0.83[CHD][hapmap];0.82[JPT][hapmap];0.83[AFR][1000 genomes]
rs1418152	0.91[ASW][hapmap];0.83[AFR][1000 genomes]
rs1418153	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs1640849	0.83[CHD][hapmap];0.82[JPT][hapmap]
rs17479856	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs17480087	0.82[JPT][hapmap]
rs17517952	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518077	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17518349	0.82[JPT][hapmap]
rs17518363	0.82[JPT][hapmap]
rs17538964	0.91[ASW][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.81[GIH][hapmap];0.91[JPT][hapmap];0.81[TSI][hapmap];0.83[AFR][1000 genomes];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17539269	0.82[JPT][hapmap]
rs17577025	0.91[ASW][hapmap];0.83[AFR][1000 genomes]
rs17577212	0.83[AFR][1000 genomes];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1829310	0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28561511	0.87[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61837634	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61837638	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs61837640	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61838191	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61838192	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61838194	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs61838197	0.82[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838199	0.95[AFR][1000 genomes];0.82[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838200	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838201	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412060	0.83[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7518292	0.83[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs9442043	0.83[AFR][1000 genomes];0.97[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	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
3	nsv518979	chr1:223468336-223488310	Weak transcription Enhancers Strong transcription	TF binding region CpG island Chromatin interactive region	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1400963	SUSD4	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223466400-223480400	Weak transcription	Pancreas	Pancrea
2	chr1:223470000-223493200	Weak transcription	Esophagus	oesophagus
3	chr1:223473000-223484400	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr1:223475800-223480800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
5	chr1:223476000-223482000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
6	chr1:223476200-223480800	Weak transcription	Thymus	Thymus
7	chr1:223476200-223481200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
8	chr1:223476200-223481600	Weak transcription	Primary T helper cells PMA-I stimulated	--

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