Variant report

Variant	rs11923553
Chromosome Location	chr3:67510633-67510634
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 60 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs11127623	0.84[AMR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11705861	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11709258	0.81[AMR][1000 genomes]
rs11710800	0.82[ASN][1000 genomes]
rs11920877	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12374036	0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12495460	0.86[ASN][1000 genomes]
rs12497043	0.83[ASN][1000 genomes]
rs12635531	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs13059103	0.87[ASN][1000 genomes]
rs13076634	0.82[ASN][1000 genomes]
rs13090999	0.87[ASN][1000 genomes]
rs13095360	0.83[ASN][1000 genomes]
rs4327406	0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4349513	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs4577484	0.83[ASN][1000 genomes]
rs4645146	0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4856782	0.83[ASN][1000 genomes]
rs4856863	0.81[ASN][1000 genomes]
rs4856864	0.82[ASN][1000 genomes]
rs4856865	0.82[ASN][1000 genomes]
rs55887942	0.81[ASN][1000 genomes]
rs56393250	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs57077433	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs60806282	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60931405	0.82[ASN][1000 genomes]
rs62256386	0.88[AMR][1000 genomes];0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256387	0.92[AMR][1000 genomes];0.85[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256391	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256392	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs62256395	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs62256396	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs62256399	0.82[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6767651	0.82[ASN][1000 genomes]
rs6768043	0.82[ASN][1000 genomes]
rs6769758	0.81[ASN][1000 genomes]
rs6770533	0.82[ASN][1000 genomes]
rs6773365	0.86[ASN][1000 genomes]
rs6773425	0.81[ASN][1000 genomes]
rs6779086	0.96[AFR][1000 genomes];0.96[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6780361	0.82[ASN][1000 genomes]
rs6789939	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6791455	0.80[ASN][1000 genomes]
rs6802566	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6805028	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs6810165	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73088910	0.93[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7429940	0.83[EUR][1000 genomes]
rs7614213	0.83[ASN][1000 genomes]
rs7620241	0.83[ASN][1000 genomes]
rs7630024	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7635366	0.87[ASN][1000 genomes]
rs7651649	0.82[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs9873407	0.88[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
6	nsv3860	chr3:67493286-67517941	Enhancers Strong transcription Weak transcription ZNF genes & repeats Genic enhancers Flanking Active TSS	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs11923553	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:48 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
2	chr3:67471600-67518800	Weak transcription	Rectal Mucosa Donor 31	rectum
3	chr3:67473400-67521000	Weak transcription	Primary T helper cells PMA-I stimulated	--
4	chr3:67473600-67542000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr3:67478200-67512200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:67482600-67527200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr3:67482600-67528600	Weak transcription	GM12878-XiMat	blood
8	chr3:67482800-67520800	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr3:67482800-67533400	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr3:67484000-67511400	Weak transcription	Fetal Lung	lung
11	chr3:67487000-67518600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
12	chr3:67487800-67512200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr3:67488000-67544200	Weak transcription	A549	lung
14	chr3:67488400-67566400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
15	chr3:67490200-67511800	Weak transcription	HSMMtube	muscle
16	chr3:67492200-67545400	Weak transcription	Fetal Intestine Small	intestine
17	chr3:67492400-67515400	Weak transcription	Primary B cells from peripheral blood	blood
18	chr3:67492400-67516600	Weak transcription	Primary T helper cells fromperipheralblood	blood
19	chr3:67498000-67534200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
20	chr3:67499400-67512000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
21	chr3:67500800-67567000	Weak transcription	Pancreas	Pancrea
22	chr3:67501200-67533600	Weak transcription	Fetal Intestine Large	intestine
23	chr3:67504000-67559800	Weak transcription	Esophagus	oesophagus
24	chr3:67504600-67518800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
25	chr3:67504800-67513400	Weak transcription	Rectal Mucosa Donor 29	rectum
26	chr3:67505800-67516200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
27	chr3:67506200-67512800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
28	chr3:67506600-67544000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
29	chr3:67507000-67511800	Weak transcription	Fetal Stomach	stomach
30	chr3:67508200-67577600	Weak transcription	Spleen	Spleen
31	chr3:67508600-67511400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
32	chr3:67508800-67542000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
33	chr3:67509000-67537200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr3:67509200-67511200	Weak transcription	Muscle Satellite Cultured Cells	--
35	chr3:67509200-67512000	Weak transcription	Gastric	stomach
36	chr3:67509200-67534400	Weak transcription	Left Ventricle	heart
37	chr3:67509400-67510800	Weak transcription	HUVEC	blood vessel
38	chr3:67509400-67511200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr3:67509600-67512600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr3:67509800-67510800	Strong transcription	HSMM	muscle
41	chr3:67509800-67511400	Weak transcription	Fetal Kidney	kidney
42	chr3:67509800-67512200	Weak transcription	Fetal Heart	heart
43	chr3:67509800-67513600	Strong transcription	Liver	Liver
44	chr3:67510000-67515600	Strong transcription	Primary B cells from cord blood	blood
45	chr3:67510400-67511000	Weak transcription	NHLF	lung
46	chr3:67510400-67511400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
47	chr3:67510400-67512200	Weak transcription	Ovary	ovary
48	chr3:67510400-67512600	Weak transcription	Primary T cells from cord blood	blood

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