Variant report

Variant	rs56067370
Chromosome Location	chr3:67593868-67593869
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 14 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:7)

rs_ID	r²[population]
rs11709337	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11929213	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12496418	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12497990	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6780493	0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs6788296	0.92[ASN][1000 genomes]
rs7618449	0.88[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 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	nsv1012416	chr3:67546244-67615531	Weak transcription Enhancers Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
6	nsv590561	chr3:67548852-67690626	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	esv3359258	chr3:67589615-67828274	Weak transcription Strong transcription Enhancers Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs56067370	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67560600-67620800	Weak transcription	Esophagus	oesophagus
2	chr3:67565600-67595800	Weak transcription	Fetal Kidney	kidney
3	chr3:67578200-67600400	Weak transcription	Lung	lung
4	chr3:67578200-67612400	Weak transcription	Spleen	Spleen
5	chr3:67578200-67634600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
6	chr3:67578600-67601800	Weak transcription	Left Ventricle	heart
7	chr3:67579200-67603400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
8	chr3:67579200-67608800	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:67579200-67620600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
10	chr3:67579400-67598200	Weak transcription	Aorta	Aorta
11	chr3:67579400-67600600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr3:67579400-67623000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
13	chr3:67579400-67633800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
14	chr3:67579400-67657600	Weak transcription	Pancreas	Pancrea
15	chr3:67579600-67601000	Weak transcription	Duodenum Mucosa	Duodenum
16	chr3:67579600-67601800	Weak transcription	Fetal Intestine Large	intestine
17	chr3:67579600-67601800	Weak transcription	Ovary	ovary
18	chr3:67580000-67606400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
19	chr3:67580800-67620200	Weak transcription	GM12878-XiMat	blood
20	chr3:67582000-67601600	Weak transcription	Rectal Mucosa Donor 31	rectum
21	chr3:67582200-67637000	Weak transcription	Rectal Smooth Muscle	rectum
22	chr3:67582400-67596400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:67582400-67609000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr3:67582400-67620400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr3:67582600-67612000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
26	chr3:67584400-67601600	Weak transcription	A549	lung
27	chr3:67586200-67597600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr3:67587000-67620200	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr3:67587400-67628000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
30	chr3:67588800-67602200	Weak transcription	Primary T helper cells fromperipheralblood	blood
31	chr3:67589000-67603000	Weak transcription	Primary T helper cells PMA-I stimulated	--
32	chr3:67589800-67615000	Weak transcription	HSMMtube	muscle
33	chr3:67591400-67597800	Weak transcription	Primary T cells from cord blood	blood
34	chr3:67591400-67600400	Weak transcription	Psoas Muscle	Psoas
35	chr3:67591400-67620200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
36	chr3:67591600-67606200	Weak transcription	Liver	Liver
37	chr3:67591600-67611200	Weak transcription	HepG2	liver
38	chr3:67592600-67600800	Weak transcription	Fetal Stomach	stomach
39	chr3:67593000-67604600	Weak transcription	Primary B cells from peripheral blood	blood
40	chr3:67593200-67594400	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr3:67593600-67594000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
42	chr3:67593600-67594200	Strong transcription	Primary T cells fromperipheralblood	blood
43	chr3:67593600-67594400	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
44	chr3:67593600-67594800	Enhancers	Muscle Satellite Cultured Cells	--
45	chr3:67593600-67594800	Enhancers	Osteobl	bone
46	chr3:67593600-67597400	Weak transcription	Primary B cells from cord blood	blood
47	chr3:67593800-67594000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
48	chr3:67593800-67594000	ZNF genes & repeats	Fetal Intestine Small	intestine
49	chr3:67593800-67596200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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