Variant report

Variant	rs2362453
Chromosome Location	chr3:67696816-67696817
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr3:67692723..67696784-chr3:67696803..67701487,5	K562	blood:
2	chr3:67693746..67699726-chr3:67701571..67705130,8	K562	blood:
3	chr3:67693669..67696019-chr3:67696200..67698241,3	MCF-7	breast:
4	chr3:67690704..67693010-chr3:67695548..67697113,2	K562	blood:
5	chr3:67686748..67688794-chr3:67696396..67698121,2	MCF-7	breast:
6	chr3:67693692..67697649-chr3:67698032..67705100,9	K562	blood:
7	chr3:67687185..67689279-chr3:67695824..67697834,2	K562	blood:

Variant related genes	Relation type
ENSG00000241316	Chromatin interaction
ENSG00000172340	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs11707967	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs11712921	0.80[EUR][1000 genomes]
rs11717561	0.80[EUR][1000 genomes]
rs11719952	0.81[EUR][1000 genomes]
rs12714500	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13065696	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs13068759	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13069212	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13069251	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13070332	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs13076100	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13077262	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs13081838	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13083820	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs13086260	0.80[EUR][1000 genomes]
rs13090197	0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13091275	0.97[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13091330	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs13092662	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs13099253	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1376028	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1376029	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1376030	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs1450345	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1814519	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1823476	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2167181	0.91[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2198015	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2198016	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2218796	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2362454	0.81[AMR][1000 genomes]
rs2362455	0.95[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62256429	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6766403	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6774971	0.81[EUR][1000 genomes]
rs6778266	0.89[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6779395	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6786211	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6787200	0.97[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6787642	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6787853	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6788874	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6790771	0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs6791337	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs6793868	0.98[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6797010	0.81[EUR][1000 genomes]
rs6797460	0.92[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6798228	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs6806285	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6806536	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6808106	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs7434004	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7610446	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7615766	0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7632886	0.80[AMR][1000 genomes]
rs7639427	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7647518	0.97[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs881948	0.83[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs881949	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs935734	0.95[AMR][1000 genomes];0.92[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9811187	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.96[ASN][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	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
2	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
3	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
4	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
5	nsv876922	chr3:67635506-67755257	Weak transcription Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Genic enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
6	nsv428739	chr3:67656829-67730379	Enhancers Strong transcription Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2362453	SUCLG2	Cis_1M	lymphoblastoid	RTeQTL
rs2362453	RP11-81N13.1	cis	Thyroid	GTEx

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:67612400-67697200	Weak transcription	Hela-S3	cervix
2	chr3:67631400-67700200	Weak transcription	K562	blood
3	chr3:67659800-67697400	Weak transcription	Colonic Mucosa	Colon
4	chr3:67660000-67697200	Weak transcription	Lung	lung
5	chr3:67660000-67697400	Weak transcription	Skeletal Muscle Male	skeletal muscle
6	chr3:67661200-67704000	Weak transcription	Fetal Kidney	kidney
7	chr3:67661400-67699400	Weak transcription	Stomach Smooth Muscle	stomach
8	chr3:67661400-67700000	Weak transcription	Ovary	ovary
9	chr3:67661400-67701000	Weak transcription	Fetal Lung	lung
10	chr3:67661400-67704000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr3:67661600-67703600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:67668400-67699600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
13	chr3:67670200-67703400	Weak transcription	Aorta	Aorta
14	chr3:67670600-67699000	Weak transcription	HUES6 Cell Line	embryonic stem cell
15	chr3:67670800-67703200	Weak transcription	Adipose Nuclei	Adipose
16	chr3:67671000-67700600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr3:67671800-67697800	Weak transcription	Dnd41	blood
18	chr3:67673800-67703400	Weak transcription	Fetal Thymus	thymus
19	chr3:67674000-67704000	Weak transcription	Fetal Muscle Trunk	muscle
20	chr3:67681400-67703600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
21	chr3:67681800-67698800	Weak transcription	HUES64 Cell Line	embryonic stem cell
22	chr3:67681800-67704200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
23	chr3:67684800-67697200	Weak transcription	Esophagus	oesophagus
24	chr3:67685400-67697600	Weak transcription	Placenta Amnion	Placenta Amnion
25	chr3:67685800-67697200	Weak transcription	Rectal Mucosa Donor 31	rectum
26	chr3:67686200-67697200	Weak transcription	Stomach Mucosa	stomach
27	chr3:67686200-67698200	Weak transcription	Right Ventricle	heart
28	chr3:67686600-67697200	Weak transcription	Duodenum Mucosa	Duodenum
29	chr3:67686600-67697200	Weak transcription	HMEC	breast
30	chr3:67686600-67697200	Weak transcription	NHLF	lung
31	chr3:67686600-67703600	Weak transcription	Fetal Heart	heart
32	chr3:67686600-67704000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
33	chr3:67686800-67697200	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr3:67686800-67698600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr3:67686800-67703400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
36	chr3:67686800-67703400	Weak transcription	H9 Cell Line	embryonic stem cell
37	chr3:67687800-67703400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
38	chr3:67688000-67703400	Weak transcription	Primary monocytes fromperipheralblood	blood
39	chr3:67688200-67697000	Weak transcription	GM12878-XiMat	blood
40	chr3:67688400-67697200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
41	chr3:67689400-67700600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
42	chr3:67689600-67704000	Weak transcription	Thymus	Thymus
43	chr3:67690000-67697400	Weak transcription	Small Intestine	intestine
44	chr3:67690800-67700200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr3:67691000-67697200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr3:67691600-67697800	Weak transcription	Placenta	Placenta
47	chr3:67691800-67697000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr3:67691800-67697000	Weak transcription	NHDF-Ad	bronchial
49	chr3:67691800-67697000	Weak transcription	Osteobl	bone
50	chr3:67691800-67700800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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