Variant report

Variant	rs274288
Chromosome Location	chr10:25254151-25254152
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr10:25253127..25256241-chr10:25256724..25259023,3	K562	blood:
2	chr10:25245492..25247955-chr10:25250126..25255906,6	K562	blood:
3	chr10:25253735..25256241-chr10:25257009..25259023,2	K562	blood:
4	chr10:25249933..25252062-chr10:25253513..25255370,2	K562	blood:
5	chr10:25245492..25247572-chr10:25252879..25256306,3	K562	blood:

Extended variants
information (count: 65 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:64)

rs_ID	r²[population]
rs1000875	0.95[CHB][hapmap]
rs10508685	0.95[CHB][hapmap]
rs10508686	0.95[CHB][hapmap];0.93[CHD][hapmap];0.80[GIH][hapmap]
rs10741072	0.82[JPT][hapmap]
rs10764515	1.00[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.98[GIH][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10764518	0.95[CHB][hapmap]
rs10764519	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap]
rs10828741	0.95[CHB][hapmap]
rs10828745	0.95[CHB][hapmap]
rs10828751	0.85[CEU][hapmap]
rs11014318	0.86[JPT][hapmap]
rs11014357	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap]
rs12249889	0.95[CHB][hapmap];0.93[CHD][hapmap];0.84[GIH][hapmap]
rs12256642	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap]
rs12761282	0.96[ASN][1000 genomes]
rs12784769	0.81[CEU][hapmap];1.00[CHB][hapmap];0.85[ASN][1000 genomes]
rs1492608	0.95[CHB][hapmap];0.98[CHD][hapmap];0.84[GIH][hapmap]
rs1546097	0.95[CHB][hapmap];0.95[CHD][hapmap];0.82[GIH][hapmap]
rs166670	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs185669	0.80[CEU][hapmap]
rs2031600	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2035888	0.86[JPT][hapmap]
rs2131276	0.95[CHB][hapmap]
rs2279547	1.00[CEU][hapmap];0.95[CHB][hapmap];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2291583	0.91[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap]
rs2307047	0.85[CEU][hapmap];0.87[CHB][hapmap];0.91[CHD][hapmap];0.84[GIH][hapmap]
rs2478091	0.82[ASN][1000 genomes]
rs274289	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs274290	0.91[ASN][1000 genomes]
rs274291	0.86[ASN][1000 genomes]
rs274292	0.86[ASN][1000 genomes]
rs274293	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274294	0.81[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs274301	0.92[CEU][hapmap];1.00[CHB][hapmap];0.82[JPT][hapmap];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs274303	0.81[ASN][1000 genomes]
rs274304	0.81[CEU][hapmap];0.81[ASN][1000 genomes]
rs274305	0.84[CEU][hapmap];0.86[CHB][hapmap];0.84[GIH][hapmap];0.85[JPT][hapmap];0.89[ASN][1000 genomes]
rs274306	0.81[ASN][1000 genomes]
rs274307	0.90[ASN][1000 genomes]
rs274308	0.81[ASN][1000 genomes]
rs274309	0.81[ASN][1000 genomes]
rs274310	0.90[ASN][1000 genomes]
rs274311	0.84[CEU][hapmap];0.86[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap];0.91[JPT][hapmap];0.82[TSI][hapmap];0.90[ASN][1000 genomes]
rs274312	0.81[ASN][1000 genomes]
rs274313	0.84[CEU][hapmap];0.86[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs274316	0.84[CEU][hapmap];0.86[JPT][hapmap];0.84[ASN][1000 genomes]
rs2818289	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3748223	0.82[JPT][hapmap]
rs4345864	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs4556443	0.89[EUR][1000 genomes]
rs4748993	0.80[CEU][hapmap];0.91[CHB][hapmap]
rs4748996	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap]
rs4749000	0.80[GIH][hapmap]
rs612482	0.88[ASN][1000 genomes]
rs6482467	0.95[CHB][hapmap];0.81[ASN][1000 genomes]
rs6482468	0.88[CEU][hapmap];0.83[CHB][hapmap]
rs7082131	0.80[ASN][1000 genomes]
rs7086282	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap]
rs7393543	0.81[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];0.98[GIH][hapmap]
rs7913853	0.95[CHB][hapmap]
rs902903	0.88[CEU][hapmap];0.82[CHB][hapmap]
rs902904	0.95[CHB][hapmap];0.95[CHD][hapmap];0.84[GIH][hapmap]
rs902905	0.95[CHB][hapmap]
rs987274	0.81[CEU][hapmap];0.95[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:1 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1053278	chr10:25140776-25269093	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs274288	THNSL1	cis	parietal	SCAN
rs274288	ANKRD9	trans	cerebellum	SCAN
rs274288	PIP4K2A	cis	parietal	SCAN
rs274288	THNSL1	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr10:25248400-25256600	Weak transcription	Fetal Brain Male	brain
2	chr10:25248400-25256600	Weak transcription	Fetal Kidney	kidney
3	chr10:25249200-25258600	Weak transcription	Brain Anterior Caudate	brain
4	chr10:25249200-25258600	Weak transcription	Brain Cingulate Gyrus	brain
5	chr10:25249200-25262200	Weak transcription	Fetal Stomach	stomach
6	chr10:25249200-25263800	Weak transcription	Ovary	ovary
7	chr10:25249400-25258200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
8	chr10:25251000-25263800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr10:25251800-25254200	Enhancers	K562	blood
10	chr10:25253200-25262000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr10:25253200-25264000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr10:25253800-25254400	Enhancers	Fetal Muscle Leg	muscle
13	chr10:25253800-25254400	Enhancers	Right Atrium	heart

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