Variant report

Variant	rs17539269
Chromosome Location	chr1:223497357-223497358
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:223471938..223473458-chr1:223497150..223499757,2	K562	blood:
2	chr1:223497129..223500114-chr1:223509294..223511393,2	K562	blood:
3	chr1:223496498..223499043-chr1:223513776..223516102,2	K562	blood:

Extended variants
information (count: 50 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10495206	0.84[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];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10495207	0.84[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10907376	0.84[CEU][hapmap];0.82[CHB][hapmap];0.94[CHD][hapmap];0.84[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.82[EUR][1000 genomes]
rs1115114	0.91[AFR][1000 genomes]
rs11261264	1.00[CHB][hapmap];0.92[JPT][hapmap];0.85[AMR][1000 genomes];0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11261270	0.91[AFR][1000 genomes]
rs12123148	1.00[CHB][hapmap];0.91[JPT][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12140453	0.84[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.86[MEX][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12564615	0.84[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap];0.91[AFR][1000 genomes];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1341988	0.82[JPT][hapmap]
rs1400959	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];0.87[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1400963	0.82[JPT][hapmap]
rs1418150	0.82[JPT][hapmap]
rs1547788	0.81[EUR][1000 genomes]
rs1640849	0.82[JPT][hapmap]
rs17162008	0.82[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs17162072	0.84[JPT][hapmap]
rs17163827	0.91[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs17479856	0.91[JPT][hapmap]
rs17480087	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17480344	0.84[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17518349	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17518363	1.00[CEU][hapmap];1.00[CHB][hapmap];0.87[CHD][hapmap];0.83[GIH][hapmap];1.00[JPT][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17538964	0.91[JPT][hapmap]
rs17539583	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	1.00[ASW][hapmap];0.88[CEU][hapmap];0.83[GIH][hapmap];0.93[MEX][hapmap];0.88[TSI][hapmap];0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17578168	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]
rs17578203	1.00[ASW][hapmap];0.83[CEU][hapmap];1.00[CHB][hapmap];0.81[CHD][hapmap];0.89[GIH][hapmap];0.92[JPT][hapmap];0.93[MEX][hapmap];1.00[MKK][hapmap];1.00[AFR][1000 genomes];0.88[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1772280	0.82[EUR][1000 genomes]
rs34150324	0.85[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs61838208	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838209	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs61838210	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs61838229	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61838230	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838231	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs61838234	0.81[EUR][1000 genomes]
rs61838235	0.81[EUR][1000 genomes]
rs61838238	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61838239	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs61838240	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838243	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs61838250	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61838252	0.83[EUR][1000 genomes]
rs61839867	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7536652	0.81[TSI][hapmap];0.81[EUR][1000 genomes]
rs7541162	0.80[EUR][1000 genomes]
rs9442042	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.95[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs17539269	SUSD4	cis	Heart Left Ventricle	GTEx
rs17539269	SUSD4	cis	parietal	SCAN
rs17539269	SUSD4	cis	cerebellum	SCAN

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:223495200-223498400	Enhancers	Fetal Thymus	thymus
2	chr1:223495600-223498400	Enhancers	Primary T cells from cord blood	blood
3	chr1:223495600-223498400	Enhancers	Thymus	Thymus
4	chr1:223495800-223498200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:223496000-223498000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
6	chr1:223496000-223498200	Enhancers	Primary T helper naive cells from peripheral blood	blood
7	chr1:223496000-223498600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
8	chr1:223496200-223497400	Weak transcription	Fetal Heart	heart
9	chr1:223496200-223498200	Enhancers	Primary T cells fromperipheralblood	blood
10	chr1:223496200-223498200	Enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:223496400-223498200	Enhancers	Primary T helper cells fromperipheralblood	blood
12	chr1:223496400-223498200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
13	chr1:223496400-223498400	Enhancers	Primary T killer memory cells from peripheral blood	blood
14	chr1:223496600-223497400	Enhancers	Primary hematopoietic stem cells	blood
15	chr1:223496800-223497600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
16	chr1:223496800-223497600	Flanking Active TSS	Dnd41	blood
17	chr1:223497200-223497400	Enhancers	Pancreatic Islets	Pancreatic Islet
18	chr1:223497200-223497600	Enhancers	Primary neutrophils fromperipheralblood	blood
19	chr1:223497200-223498000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
20	chr1:223497200-223504200	Weak transcription	Right Atrium	heart
21	chr1:223497200-223512600	Weak transcription	Pancreas	Pancrea

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