Variant report

Variant	rs11710800
Chromosome Location	chr3:67466303-67466304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 44 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs11127623	0.82[ASN][1000 genomes]
rs11920877	0.82[ASN][1000 genomes]
rs11923553	0.82[ASN][1000 genomes]
rs12374036	0.87[ASN][1000 genomes]
rs12495460	0.92[ASN][1000 genomes]
rs12497043	0.99[ASN][1000 genomes]
rs13059103	0.92[ASN][1000 genomes]
rs13076634	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13090999	0.92[ASN][1000 genomes]
rs13095360	0.98[ASN][1000 genomes]
rs4327406	0.87[ASN][1000 genomes]
rs4577484	0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4645146	0.85[ASN][1000 genomes]
rs4856782	0.83[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs4856863	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs4856864	0.98[ASN][1000 genomes]
rs4856865	0.84[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs55887942	0.85[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs55957459	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs60806282	0.83[ASN][1000 genomes]
rs60931405	0.83[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62256379	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	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6768043	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6769758	0.98[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6770533	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs6773365	0.95[ASN][1000 genomes]
rs6773425	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6779086	0.88[ASN][1000 genomes]
rs6780361	0.98[ASN][1000 genomes]
rs6791455	0.97[ASN][1000 genomes]
rs6810165	0.87[ASN][1000 genomes]
rs7614213	0.85[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs7620241	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7635366	0.92[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11710800	SUCLG2	cis	multi-tissue	Pritchard
rs11710800	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL
rs11710800	SUCLG2	cis	lesional skin	skin_eQTL

Chromatin state (count:57 , 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	chr3:67424600-67471000	Weak transcription	Colonic Mucosa	Colon
4	chr3:67425000-67474200	Weak transcription	Gastric	stomach
5	chr3:67431600-67469400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr3:67435400-67467200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr3:67435600-67509800	Weak transcription	Ovary	ovary
8	chr3:67435600-67534200	Weak transcription	Aorta	Aorta
9	chr3:67440000-67470600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr3:67441200-67471600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:67442800-67467200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr3:67442800-67478000	Weak transcription	Lung	lung
13	chr3:67449400-67486600	Weak transcription	Fetal Stomach	stomach
14	chr3:67450600-67467200	Weak transcription	Osteobl	bone
15	chr3:67450600-67470200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
16	chr3:67450600-67470400	Weak transcription	A549	lung
17	chr3:67451200-67466600	Weak transcription	Duodenum Smooth Muscle	Duodenum
18	chr3:67451200-67470400	Weak transcription	Rectal Mucosa Donor 31	rectum
19	chr3:67451200-67487800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr3:67451400-67470200	Weak transcription	Dnd41	blood
21	chr3:67453600-67470400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr3:67454000-67469800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr3:67454600-67478000	Weak transcription	Fetal Intestine Small	intestine
24	chr3:67455200-67470000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr3:67455200-67470400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
26	chr3:67458600-67470600	Weak transcription	HSMM	muscle
27	chr3:67459000-67468000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
28	chr3:67459200-67471000	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:67459600-67470200	Weak transcription	Liver	Liver
30	chr3:67459800-67468800	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:67459800-67470200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
32	chr3:67460000-67468600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
33	chr3:67460000-67470200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr3:67460000-67470400	Weak transcription	Fetal Intestine Large	intestine
35	chr3:67463000-67487400	Weak transcription	Pancreas	Pancrea
36	chr3:67463200-67466400	Weak transcription	Right Atrium	heart
37	chr3:67463200-67466600	Strong transcription	Primary T cells from cord blood	blood
38	chr3:67463200-67478400	Weak transcription	Psoas Muscle	Psoas
39	chr3:67463200-67484200	Weak transcription	Right Ventricle	heart
40	chr3:67463400-67466600	Strong transcription	Primary B cells from cord blood	blood
41	chr3:67463600-67466600	Strong transcription	Primary T cells fromperipheralblood	blood
42	chr3:67465200-67466600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr3:67465200-67466600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:67465400-67466400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr3:67465400-67466600	Enhancers	Fetal Heart	heart
46	chr3:67465400-67489600	Weak transcription	Stomach Smooth Muscle	stomach
47	chr3:67465800-67466600	Enhancers	NHLF	lung
48	chr3:67465800-67467600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr3:67466000-67466400	Genic enhancers	Fetal Lung	lung
50	chr3:67466000-67466600	Strong transcription	Primary B cells from peripheral blood	blood

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