Variant report

Variant	rs6768043
Chromosome Location	chr3:67486021-67486022
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs11127623	0.82[ASN][1000 genomes]
rs11710800	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11920877	0.82[ASN][1000 genomes]
rs11923553	0.82[ASN][1000 genomes]
rs12374036	0.87[ASN][1000 genomes]
rs12495460	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12497043	0.90[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13059103	0.86[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13076634	0.98[ASN][1000 genomes]
rs13090999	0.88[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs13095360	0.93[AMR][1000 genomes];0.87[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4327406	0.87[ASN][1000 genomes]
rs4577484	0.96[ASN][1000 genomes]
rs4645146	0.85[ASN][1000 genomes]
rs4856782	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4856863	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4856864	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4856865	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55887942	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs55957459	0.81[AFR][1000 genomes]
rs60806282	0.83[ASN][1000 genomes]
rs60931405	0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs62256379	0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62256386	0.88[ASN][1000 genomes]
rs62256387	0.88[ASN][1000 genomes]
rs62256391	0.82[ASN][1000 genomes]
rs62256392	0.83[ASN][1000 genomes]
rs6767651	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6769758	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6770533	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6773365	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6773425	0.98[ASN][1000 genomes]
rs6779086	0.88[ASN][1000 genomes]
rs6780361	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6791455	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6810165	0.87[ASN][1000 genomes]
rs7614213	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620241	0.80[AFR][1000 genomes];0.97[ASN][1000 genomes]
rs7635366	0.86[AMR][1000 genomes];0.93[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
rs6768043	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:41 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67509800	Weak transcription	Ovary	ovary
2	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
3	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
4	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr3:67463000-67487400	Weak transcription	Pancreas	Pancrea
6	chr3:67465400-67489600	Weak transcription	Stomach Smooth Muscle	stomach
7	chr3:67466600-67486200	Weak transcription	Left Ventricle	heart
8	chr3:67466600-67508400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr3:67471200-67487600	Weak transcription	A549	lung
10	chr3:67471200-67503800	Weak transcription	Rectal Mucosa Donor 29	rectum
11	chr3:67471400-67497600	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
12	chr3:67471600-67486600	Weak transcription	Duodenum Smooth Muscle	Duodenum
13	chr3:67471600-67487600	Weak transcription	Fetal Intestine Large	intestine
14	chr3:67471600-67489200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
16	chr3:67471800-67487800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
17	chr3:67472000-67506200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
18	chr3:67472000-67509800	Weak transcription	HSMM	muscle
19	chr3:67473400-67492200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
20	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
21	chr3:67473600-67487400	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr3:67473600-67487400	Weak transcription	Liver	Liver
23	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
24	chr3:67478200-67512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
25	chr3:67478600-67492000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr3:67481400-67493400	Weak transcription	Muscle Satellite Cultured Cells	--
27	chr3:67482400-67486200	Weak transcription	Adipose Nuclei	Adipose
28	chr3:67482600-67527200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
29	chr3:67482600-67528600	Weak transcription	GM12878-XiMat	blood
30	chr3:67482800-67503800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr3:67482800-67520800	Weak transcription	Primary T cells fromperipheralblood	blood
32	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
33	chr3:67484000-67487000	Weak transcription	Gastric	stomach
34	chr3:67484000-67492000	Weak transcription	Primary T helper cells fromperipheralblood	blood
35	chr3:67484000-67511400	Weak transcription	Fetal Lung	lung
36	chr3:67485000-67486600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
37	chr3:67485000-67493200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr3:67485400-67487000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
39	chr3:67485600-67486400	Weak transcription	Primary T cells from cord blood	blood
40	chr3:67485600-67490200	Weak transcription	Primary B cells from peripheral blood	blood
41	chr3:67485800-67503800	Weak transcription	Primary B cells from cord blood	blood

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