Variant report

Variant	rs576
Chromosome Location	chr3:70016467-70016468
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:70012809..70015718-chr3:70015918..70017994,3	K562	blood:
2	chr3:70013897..70016716-chr3:70049706..70051313,2	K562	blood:
3	chr3:70013471..70015718-chr3:70015918..70017994,2	K562	blood:

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:67)

rs_ID	r²[population]
rs1021413	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.95[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11718882	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11923682	0.84[ASN][1000 genomes]
rs11926368	0.83[ASN][1000 genomes]
rs12495230	0.83[CHD][hapmap]
rs12639523	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1491687	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1491688	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491689	0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1491695	0.80[CHB][hapmap];0.83[CHD][hapmap]
rs1491698	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs1546075	0.84[ASN][1000 genomes]
rs17727959	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1844877	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1873583	0.83[ASN][1000 genomes]
rs1873584	0.83[ASN][1000 genomes]
rs1907646	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs1907647	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2131026	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2172211	1.00[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28524674	0.86[ASN][1000 genomes]
rs2874270	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs34790356	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs35180789	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs35416604	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35996477	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs36125122	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs3772111	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3821364	0.95[CEU][hapmap];0.90[CHB][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.86[TSI][hapmap];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs3967688	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4635708	0.93[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4855331	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855453	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];1.00[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855454	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855455	1.00[CEU][hapmap];0.95[CHB][hapmap];0.80[JPT][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4855456	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs55842620	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs56351003	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6549254	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549255	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6549256	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6549257	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549258	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549259	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6549260	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6549261	0.90[CHB][hapmap];0.97[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs6549262	0.84[ASN][1000 genomes]
rs6771970	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs6784666	0.84[ASN][1000 genomes]
rs6809508	0.84[ASN][1000 genomes]
rs704246	0.95[CEU][hapmap];0.95[CHB][hapmap];0.80[CHD][hapmap];0.90[MEX][hapmap];0.93[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs73119519	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7429562	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7431913	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs902711	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs902712	0.94[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs923702	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs9310178	0.90[CHB][hapmap];0.95[JPT][hapmap];0.83[ASN][1000 genomes]
rs9310179	0.90[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];0.84[ASN][1000 genomes]
rs9310180	0.80[CHB][hapmap]
rs956436	0.83[ASN][1000 genomes]
rs9840397	0.84[ASN][1000 genomes]
rs9840590	0.86[ASN][1000 genomes]
rs9849031	0.84[ASN][1000 genomes]
rs9851891	0.80[CHB][hapmap]
rs9863457	0.84[ASN][1000 genomes]
rs9868203	0.84[ASN][1000 genomes]

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	nsv533396	chr3:69964029-70538306	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs576	GXYLT2	cis	parietal	SCAN

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:69981800-70016800	Weak transcription	K562	blood
2	chr3:69998200-70017600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr3:70001600-70017200	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr3:70003800-70016600	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
5	chr3:70004600-70017000	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:70005400-70017000	Weak transcription	Hela-S3	cervix
7	chr3:70006000-70017400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr3:70007200-70017400	Weak transcription	Fetal Muscle Trunk	muscle
9	chr3:70009000-70021200	Weak transcription	Rectal Smooth Muscle	rectum
10	chr3:70009600-70018800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr3:70009800-70017200	Weak transcription	Pancreas	Pancrea
12	chr3:70009800-70018800	Weak transcription	Colon Smooth Muscle	Colon
13	chr3:70010000-70016600	Weak transcription	Brain Anterior Caudate	brain
14	chr3:70010200-70021200	Weak transcription	HSMMtube	muscle
15	chr3:70010200-70022800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr3:70010200-70024000	Weak transcription	Fetal Kidney	kidney
17	chr3:70014400-70021200	Weak transcription	Stomach Smooth Muscle	stomach
18	chr3:70014400-70021400	Weak transcription	Psoas Muscle	Psoas
19	chr3:70014400-70021400	Weak transcription	Skeletal Muscle Male	skeletal muscle
20	chr3:70014600-70019600	Weak transcription	Left Ventricle	heart
21	chr3:70014600-70021200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr3:70014800-70020000	Weak transcription	Monocytes-CD14+_RO01746	blood
23	chr3:70015000-70016600	Weak transcription	Liver	Liver
24	chr3:70015000-70016800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:70015000-70024600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr3:70015600-70017200	Strong transcription	Skeletal Muscle Female	skeletal muscle
27	chr3:70015600-70018200	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:70015600-70019000	Weak transcription	Adipose Nuclei	Adipose
29	chr3:70015600-70020000	Weak transcription	Primary monocytes fromperipheralblood	blood
30	chr3:70015800-70016600	Enhancers	Brain Inferior Temporal Lobe	brain
31	chr3:70015800-70017000	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
32	chr3:70015800-70017000	Strong transcription	Ovary	ovary
33	chr3:70015800-70017200	Enhancers	Brain Substantia Nigra	brain
34	chr3:70015800-70017400	Enhancers	Brain Angular Gyrus	brain
35	chr3:70016400-70016600	Active TSS	Brain Hippocampus Middle	brain

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