Variant report

Variant	rs1065399
Chromosome Location	chr3:67426125-67426126
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 20 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1065400	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1065401	0.80[GIH][hapmap]
rs12330438	0.83[CEU][hapmap]
rs12634424	0.93[ASN][1000 genomes]
rs12637020	0.93[ASN][1000 genomes]
rs1387856	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs1979640	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2171933	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2171934	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779718	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7620956	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7642866	0.89[ASN][1000 genomes]
rs902320	0.83[ASN][1000 genomes]
rs9811979	0.91[ASN][1000 genomes]
rs9833822	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
rs1065399	SUCLG2	cis	lymphoblastoid	seeQTL

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67412400-67453000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr3:67413200-67441800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr3:67414200-67438800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr3:67414400-67426200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
5	chr3:67414400-67470800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr3:67417200-67432600	Weak transcription	A549	lung
7	chr3:67417400-67435800	Weak transcription	Primary B cells from cord blood	blood
8	chr3:67418400-67432600	Weak transcription	Muscle Satellite Cultured Cells	--
9	chr3:67418600-67434600	Weak transcription	Osteobl	bone
10	chr3:67418600-67442600	Weak transcription	Dnd41	blood
11	chr3:67420000-67432600	Weak transcription	Psoas Muscle	Psoas
12	chr3:67420200-67426200	Weak transcription	Aorta	Aorta
13	chr3:67420200-67426200	Weak transcription	Fetal Intestine Large	intestine
14	chr3:67420200-67426200	Weak transcription	Left Ventricle	heart
15	chr3:67420200-67426400	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr3:67420200-67427800	Weak transcription	Lung	lung
17	chr3:67420200-67429400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr3:67420200-67430400	Weak transcription	Pancreas	Pancrea
19	chr3:67420200-67432200	Weak transcription	Cortex derived primary cultured neurospheres	brain
20	chr3:67420200-67432600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr3:67420200-67432800	Weak transcription	Right Ventricle	heart
22	chr3:67420200-67437000	Weak transcription	Spleen	Spleen
23	chr3:67420200-67441600	Weak transcription	Rectal Mucosa Donor 31	rectum
24	chr3:67420200-67441800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
25	chr3:67420200-67449600	Weak transcription	HSMM	muscle
26	chr3:67420200-67452000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr3:67420200-67479400	Weak transcription	Esophagus	oesophagus
28	chr3:67420400-67426200	Weak transcription	Primary B cells from peripheral blood	blood
29	chr3:67420400-67426200	Weak transcription	Ovary	ovary
30	chr3:67420400-67428800	Weak transcription	Rectal Mucosa Donor 29	rectum
31	chr3:67421000-67434600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
32	chr3:67421000-67434800	Weak transcription	Adipose Nuclei	Adipose
33	chr3:67421200-67433200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
34	chr3:67421400-67426200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr3:67421400-67426200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr3:67421400-67426400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
37	chr3:67421800-67441800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr3:67422600-67426800	Strong transcription	Liver	Liver
39	chr3:67422600-67437200	Weak transcription	HMEC	breast
40	chr3:67422800-67439600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
41	chr3:67423200-67441800	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr3:67423600-67427000	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
43	chr3:67424000-67429200	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr3:67424000-67432600	Weak transcription	Fetal Muscle Leg	muscle
45	chr3:67424200-67426200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr3:67424200-67426600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr3:67424200-67427600	Strong transcription	Primary T helper cells fromperipheralblood	blood
48	chr3:67424400-67435600	Weak transcription	GM12878-XiMat	blood
49	chr3:67424600-67426200	Weak transcription	Fetal Lung	lung
50	chr3:67424600-67427200	Strong transcription	Primary T helper cells PMA-I stimulated	--

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