Variant report

Variant	rs62256379
Chromosome Location	chr3:67457577-67457578
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs11710800	0.91[ASN][1000 genomes]
rs12495460	0.81[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs12497043	0.84[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs13059103	0.84[ASN][1000 genomes]
rs13076634	0.91[ASN][1000 genomes]
rs13090999	0.84[ASN][1000 genomes]
rs13095360	0.82[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs4327406	0.80[ASN][1000 genomes]
rs4577484	0.93[ASN][1000 genomes]
rs4645146	0.81[ASN][1000 genomes]
rs4856782	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4856863	0.88[AMR][1000 genomes];0.84[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4856864	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4856865	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs55887942	0.89[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs60931405	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs62256386	0.81[ASN][1000 genomes]
rs62256387	0.81[ASN][1000 genomes]
rs6767651	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6768043	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6769758	0.89[ASN][1000 genomes]
rs6770533	0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6773365	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs6773425	0.89[ASN][1000 genomes]
rs6779086	0.81[ASN][1000 genomes]
rs6780361	0.85[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6791455	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6810165	0.80[ASN][1000 genomes]
rs7614213	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7620241	0.92[ASN][1000 genomes]
rs7635366	0.84[ASN][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
rs62256379	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

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	chr3:67448800-67459200	Weak transcription	HUVEC	blood vessel
28	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
29	chr3:67449800-67459400	Strong transcription	Primary T cells from cord blood	blood
30	chr3:67450000-67458600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr3:67450400-67464000	Weak transcription	Small Intestine	intestine
32	chr3:67450600-67467200	Weak transcription	Osteobl	bone
33	chr3:67450600-67470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
34	chr3:67450600-67470400	Weak transcription	A549	lung
35	chr3:67451200-67457600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr3:67451200-67457600	Weak transcription	Duodenum Mucosa	Duodenum
37	chr3:67451200-67458000	Weak transcription	Adipose Nuclei	Adipose
38	chr3:67451200-67458000	Weak transcription	Fetal Intestine Large	intestine
39	chr3:67451200-67460400	Weak transcription	GM12878-XiMat	blood
40	chr3:67451200-67462600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
41	chr3:67451200-67466200	Weak transcription	NHDF-Ad	bronchial
42	chr3:67451200-67466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
43	chr3:67451200-67470400	Weak transcription	Rectal Mucosa Donor 31	rectum
44	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
45	chr3:67451400-67459200	Weak transcription	Sigmoid Colon	Sigmoid Colon
46	chr3:67451400-67464600	Weak transcription	Skeletal Muscle Female	skeletal muscle
47	chr3:67451400-67466200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:67451400-67470200	Weak transcription	Dnd41	blood
49	chr3:67453000-67457800	Weak transcription	Monocytes-CD14+_RO01746	blood
50	chr3:67453200-67458000	Weak transcription	Cortex derived primary cultured neurospheres	brain

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