Variant report

Variant	rs9824745
Chromosome Location	chr3:67459492-67459493
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:67457865..67460434-chr3:67463200..67466004,2	K562	blood:

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs12489223	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs12489897	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4320072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[CHD][hapmap];0.83[GIH][hapmap];0.82[JPT][hapmap];0.95[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.82[YRI][hapmap];0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4334653	0.81[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs4377498	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4455333	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4515060	0.84[AFR][1000 genomes];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4856787	0.87[EUR][1000 genomes]
rs6548542	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7623396	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs7645948	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9868494	0.89[EUR][1000 genomes]
rs9880271	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs9880590	0.82[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1007093	chr3:67113534-67602973	Weak transcription ZNF genes & repeats Enhancers Strong transcription Active TSS Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv470638	chr3:67367341-67814738	Weak transcription ZNF genes & repeats Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
3	nsv460700	chr3:67393629-67712970	Genic enhancers Enhancers Flanking Active TSS Weak transcription Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
4	nsv590560	chr3:67393629-67712970	Weak transcription Flanking Bivalent TSS/Enh Enhancers Active TSS Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
5	nsv834719	chr3:67396626-67589852	Strong transcription Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9824745	SUCLG2	cis	multi-tissue	Pritchard

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67414400-67470800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
2	chr3:67420200-67479400	Weak transcription	Esophagus	oesophagus
3	chr3:67424600-67466000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:67424600-67471000	Weak transcription	Colonic Mucosa	Colon
5	chr3:67425000-67465200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
6	chr3:67425000-67474200	Weak transcription	Gastric	stomach
7	chr3:67427000-67462800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr3:67431600-67469400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr3:67433600-67465800	Weak transcription	NHLF	lung
10	chr3:67435000-67466000	Weak transcription	Muscle Satellite Cultured Cells	--
11	chr3:67435400-67462800	Weak transcription	HSMMtube	muscle
12	chr3:67435400-67467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
13	chr3:67435600-67463200	Weak transcription	Fetal Lung	lung
14	chr3:67435600-67509800	Weak transcription	Ovary	ovary
15	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
16	chr3:67435800-67462800	Weak transcription	Fetal Muscle Leg	muscle
17	chr3:67436000-67462800	Weak transcription	Right Ventricle	heart
18	chr3:67437400-67462200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
19	chr3:67440000-67470600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr3:67441200-67471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr3:67441800-67460200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr3:67442800-67465400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
23	chr3:67442800-67467200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr3:67442800-67478000	Weak transcription	Lung	lung
25	chr3:67443000-67462600	Weak transcription	Skeletal Muscle Male	skeletal muscle
26	chr3:67446800-67460600	Weak transcription	Placenta	Placenta
27	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
28	chr3:67450400-67464000	Weak transcription	Small Intestine	intestine
29	chr3:67450600-67467200	Weak transcription	Osteobl	bone
30	chr3:67450600-67470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
31	chr3:67450600-67470400	Weak transcription	A549	lung
32	chr3:67451200-67460400	Weak transcription	GM12878-XiMat	blood
33	chr3:67451200-67462600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
34	chr3:67451200-67466200	Weak transcription	NHDF-Ad	bronchial
35	chr3:67451200-67466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
36	chr3:67451200-67470400	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr3:67451400-67464600	Weak transcription	Skeletal Muscle Female	skeletal muscle
39	chr3:67451400-67466200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr3:67451400-67470200	Weak transcription	Dnd41	blood
41	chr3:67453600-67470400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
42	chr3:67454000-67460000	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr3:67454000-67469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr3:67454600-67478000	Weak transcription	Fetal Intestine Small	intestine
45	chr3:67455200-67470000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
46	chr3:67455200-67470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
47	chr3:67455800-67466200	Weak transcription	Left Ventricle	heart
48	chr3:67456800-67459800	Strong transcription	Primary T helper cells fromperipheralblood	blood
49	chr3:67456800-67460000	Strong transcription	Primary B cells from cord blood	blood
50	chr3:67456800-67460000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood

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