Variant report

Variant	rs13100261
Chromosome Location	chr3:42643935-42643936
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	JUN	chr3:42642947-42644000	K562	blood:	n/a	n/a
2	POLR2A	chr3:42641593-42644059	K562	blood:	n/a	n/a
3	NR3C1	chr3:42643725-42643994	ECC-1	luminal epithelium:	n/a	n/a
4	JUND	chr3:42643434-42644100	K562	blood:	n/a	n/a
5	FOS	chr3:42643538-42644039	MCF10A-Er-Src	breast:	n/a	n/a
6	JUND	chr3:42643729-42644064	HepG2	liver:	n/a	n/a
7	CEBPB	chr3:42643705-42644059	ECC-1	luminal epithelium:	n/a	chr3:42643867-42643878
8	STAT3	chr3:42643835-42644063	MCF10A-Er-Src	breast:	n/a	n/a
9	CTCF	chr3:42643800-42643950	GM12864	blood:	n/a	n/a
10	TEAD4	chr3:42641408-42644046	K562	blood:	n/a	n/a
11	STAT3	chr3:42643165-42644091	MCF10A-Er-Src	breast:	n/a	n/a
12	MYC	chr3:42643374-42644033	MCF10A-Er-Src	breast:	n/a	n/a
13	TEAD4	chr3:42643190-42643985	K562	blood:	n/a	n/a
14	STAT3	chr3:42643704-42644108	MCF10A-Er-Src	breast:	n/a	n/a
15	TEAD4	chr3:42643588-42644143	ECC-1	luminal epithelium:	n/a	n/a
16	FOS	chr3:42643702-42643935	MCF10A-Er-Src	breast:	n/a	n/a
17	E2F4	chr3:42643439-42644109	MCF10A-Er-Src	breast:	n/a	n/a
18	ARID3A	chr3:42642770-42644222	K562	blood:	n/a	n/a
19	CEBPB	chr3:42643727-42644010	Hela-S3	cervix:	n/a	chr3:42643867-42643878
20	CEBPB	chr3:42643689-42644108	ECC-1	luminal epithelium:	n/a	chr3:42643867-42643878
21	CEBPB	chr3:42643748-42644032	HepG2	liver:	n/a	chr3:42643867-42643878
22	REST	chr3:42641257-42643965	H1-neurons	neurons:	n/a	chr3:42641841-42641848
23	FOS	chr3:42643480-42643994	MCF10A-Er-Src	breast:	n/a	n/a
24	STAT3	chr3:42643645-42644122	MCF10A-Er-Src	breast:	n/a	n/a
25	IRF1	chr3:42641270-42643993	K562	blood:	n/a	chr3:42641807-42641819 chr3:42641804-42641818 chr3:42641829-42641838

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:42604560..42606277-chr3:42641170..42643967,2	K562	blood:
2	chr3:42604086..42606277-chr3:42642467..42644274,2	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SS18L2-2	chr3:42642476-42644548	NONHSAT089241

Variant related genes	Relation type
SEC22C	TF binding region
ENSG00000093183	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs13064597	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13067987	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13085143	1.00[CEU][hapmap];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13086680	0.91[EUR][1000 genomes]
rs17030458	0.81[EUR][1000 genomes]
rs2290976	0.90[CEU][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes]
rs339705	0.89[CEU][hapmap]
rs339708	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs34077739	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34196076	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34243788	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34721465	0.90[EUR][1000 genomes]
rs35216140	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35384559	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35871059	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs36043081	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3733059	0.93[EUR][1000 genomes]
rs3733061	0.91[EUR][1000 genomes]
rs3900780	0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55959327	1.00[AMR][1000 genomes];0.92[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55994846	1.00[ASN][1000 genomes]
rs56047094	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58645732	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58825152	1.00[ASN][1000 genomes]
rs60535002	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs66933062	1.00[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67174294	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs67583158	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6771105	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6778982	1.00[CEU][hapmap]
rs67832425	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6790204	1.00[CEU][hapmap];0.88[TSI][hapmap];0.83[EUR][1000 genomes]
rs6794643	1.00[ASN][1000 genomes]
rs6797491	1.00[CEU][hapmap];0.83[TSI][hapmap];0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6797545	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs68004576	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs71323162	1.00[ASN][1000 genomes]
rs72864022	1.00[ASN][1000 genomes]
rs73067957	1.00[ASN][1000 genomes]
rs73829255	0.81[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7614219	1.00[CEU][hapmap];1.00[ASN][1000 genomes]
rs7616701	1.00[CEU][hapmap];0.83[TSI][hapmap];1.00[ASN][1000 genomes]
rs7623867	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1002944	chr3:42559762-42728909	Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	41 gene(s)	inside rSNPs	diseases
2	nsv876730	chr3:42643935-42667936	Strong transcription Enhancers Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13100261	SEC22C	cis	Muscle Skeletal	GTEx

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:42641200-42644000	Active TSS	ES-I3 Cell Line	embryonic stem cell
2	chr3:42641200-42644000	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr3:42641200-42644000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr3:42641200-42644200	Active TSS	HUES48 Cell Line	embryonic stem cell
5	chr3:42641200-42644200	Active TSS	HMEC	breast
6	chr3:42641400-42644000	Active TSS	Left Ventricle	heart
7	chr3:42642200-42644000	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr3:42642600-42644000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr3:42642800-42644000	Flanking Active TSS	Primary hematopoietic stem cells	blood
10	chr3:42642800-42644000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 2	blood
11	chr3:42642800-42644000	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
12	chr3:42642800-42644000	Flanking Active TSS	Brain Hippocampus Middle	brain
13	chr3:42642800-42644000	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
14	chr3:42642800-42644000	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
15	chr3:42642800-42644000	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
16	chr3:42642800-42644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr3:42642800-42646200	Weak transcription	Spleen	Spleen
18	chr3:42643000-42644000	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
19	chr3:42643000-42644000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
20	chr3:42643000-42644000	Flanking Active TSS	Primary T killer memory cells from peripheral blood	blood
21	chr3:42643000-42644000	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
22	chr3:42643000-42644000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
23	chr3:42643000-42644000	Flanking Active TSS	Adipose Nuclei	Adipose
24	chr3:42643000-42644000	Flanking Active TSS	Liver	Liver
25	chr3:42643000-42644000	Flanking Active TSS	Brain Substantia Nigra	brain
26	chr3:42643000-42644000	Flanking Active TSS	Duodenum Mucosa	Duodenum
27	chr3:42643000-42644000	Flanking Active TSS	Stomach Smooth Muscle	stomach
28	chr3:42643000-42644000	Flanking Active TSS	NHEK	skin
29	chr3:42643000-42644000	Flanking Active TSS	Osteobl	bone
30	chr3:42643000-42644200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr3:42643000-42644200	Flanking Active TSS	Brain Angular Gyrus	brain
32	chr3:42643000-42644200	Flanking Active TSS	Brain Anterior Caudate	brain
33	chr3:42643000-42644400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
34	chr3:42643000-42646200	Weak transcription	Pancreas	Pancrea
35	chr3:42643000-42650000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
36	chr3:42643000-42650000	Weak transcription	Esophagus	oesophagus
37	chr3:42643200-42644000	Flanking Active TSS	iPS-18 Cell Line	embryonic stem cell
38	chr3:42643200-42644000	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
39	chr3:42643200-42644000	Flanking Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
40	chr3:42643200-42644000	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
41	chr3:42643200-42644000	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
42	chr3:42643200-42644000	Flanking Active TSS	Fetal Lung	lung
43	chr3:42643200-42644200	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
44	chr3:42643200-42644200	Enhancers	Primary neutrophils fromperipheralblood	blood
45	chr3:42643200-42644400	Enhancers	Primary B cells from peripheral blood	blood
46	chr3:42643200-42644600	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
47	chr3:42643200-42644800	Enhancers	Sigmoid Colon	Sigmoid Colon
48	chr3:42643200-42644800	Enhancers	Small Intestine	intestine
49	chr3:42643200-42648400	Weak transcription	Placenta	Placenta
50	chr3:42643200-42649600	Weak transcription	Lung	lung

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