Variant report

Variant	rs13138942
Chromosome Location	chr4:26866763-26866764
allele	C/T
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	POLR2A	chr4:26866609-26867026	GM12891	blood:	n/a	n/a
2	ARID3A	chr4:26866478-26866930	K562	blood:	n/a	n/a
3	ATF1	chr4:26866545-26866837	K562	blood:	n/a	n/a
4	TBP	chr4:26866481-26866919	GM12878	blood:	n/a	n/a
5	POLR2A	chr4:26866575-26867125	K562	blood:	n/a	n/a
6	TBP	chr4:26866526-26866862	K562	blood:	n/a	n/a
7	IRF3	chr4:26866596-26866798	GM12878	blood:	n/a	chr4:26866751-26866765 chr4:26866747-26866761 chr4:26866751-26866761
8	POLR2A	chr4:26866669-26866799	MCF10A-Er-Src	breast:	n/a	n/a
9	GATA3	chr4:26866757-26867049	SH-SY5Y	brain:	n/a	n/a
10	POLR2A	chr4:26866623-26867096	GM12891	blood:	n/a	n/a
11	EP300	chr4:26866550-26866840	GM12878	blood:	n/a	chr4:26866746-26866760 chr4:26866752-26866766

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:26861373..26864331-chr4:26865426..26869825,6	K562	blood:
2	chr4:26864497..26869713-chr4:26871452..26874672,4	K562	blood:

Variant related genes	Relation type
ENSG00000240005	TF binding region
ENSG00000240005	Chromatin interaction
ENSG00000109689	Chromatin interaction

Extended variants
information (count: 51 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:47)

rs_ID	r²[population]
rs10029307	0.82[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs11729927	0.90[ASN][1000 genomes]
rs11730235	0.89[CHB][hapmap];1.00[JPT][hapmap];0.90[ASN][1000 genomes]
rs11734308	0.85[ASN][1000 genomes]
rs11737218	0.82[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11943948	0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12641261	0.96[ASN][1000 genomes]
rs12644073	0.82[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs12646473	0.89[CHB][hapmap];0.95[JPT][hapmap];0.96[ASN][1000 genomes]
rs12650172	0.83[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs13116341	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs13139464	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28497454	0.89[ASN][1000 genomes]
rs28520489	0.87[ASN][1000 genomes]
rs34996346	0.82[AFR][1000 genomes];0.91[AMR][1000 genomes];0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3792685	0.82[CHB][hapmap];0.89[JPT][hapmap];0.82[ASN][1000 genomes]
rs3924178	0.87[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.80[AMR][1000 genomes];0.87[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4274829	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4407490	0.83[CEU][hapmap];0.83[CHB][hapmap];0.89[JPT][hapmap];0.80[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4505809	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4519790	0.87[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.82[AMR][1000 genomes];0.88[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4532223	0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4557250	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4557251	0.94[ASN][1000 genomes]
rs57663175	0.88[ASN][1000 genomes]
rs57686546	0.89[ASN][1000 genomes]
rs58075729	0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs58968032	0.95[ASN][1000 genomes]
rs60890366	0.87[ASN][1000 genomes]
rs61047003	0.85[ASN][1000 genomes]
rs62302532	0.87[ASN][1000 genomes]
rs62302533	0.85[ASN][1000 genomes]
rs62302535	0.84[ASN][1000 genomes]
rs6448479	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.86[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6448484	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6448488	0.89[CHB][hapmap];0.95[JPT][hapmap];0.85[ASN][1000 genomes]
rs6815719	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6833053	0.82[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs6833895	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6835631	0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6844153	0.89[CHB][hapmap];0.94[JPT][hapmap];0.87[ASN][1000 genomes]
rs6853032	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73116683	0.85[ASN][1000 genomes]
rs73811400	0.95[ASN][1000 genomes]
rs73813220	0.91[ASN][1000 genomes]
rs7655686	0.91[ASN][1000 genomes]
rs9790789	0.95[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv470021	chr4:26721578-27067027	Active TSS Strong transcription Enhancers Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
2	nsv1001306	chr4:26821511-26955344	Weak transcription Flanking Active TSS Enhancers Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv461312	chr4:26844674-27078376	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent/Poised TSS Strong transcription ZNF genes & repeats Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv593872	chr4:26844674-27078376	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs13138942	RP11-293A21.1	cis	Heart Left Ventricle	GTEx
rs13138942	RP11-293A21.1	cis	Muscle Skeletal	GTEx
rs13138942	RP11-293A21.1	cis	Thyroid	GTEx
rs13138942	RP11-293A21.1	cis	Adipose Subcutaneous	GTEx
rs13138942	RP11-293A21.1	cis	Esophagus Muscularis	GTEx
rs13138942	STIM2	Cis_1M	lymphoblastoid	RTeQTL
rs13138942	RP11-293A21.1	cis	Esophagus Mucosa	GTEx
rs13138942	RP11-293A21.1	cis	lung	GTEx
rs13138942	RP11-293A21.1	cis	Skin Sun Exposed Lower leg	GTEx

Chromatin state (count:103 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:26861800-26867000	Active TSS	Ovary	ovary
2	chr4:26863800-26866800	Weak transcription	Stomach Mucosa	stomach
3	chr4:26863800-26869400	Weak transcription	Pancreas	Pancrea
4	chr4:26863800-26869400	Weak transcription	Sigmoid Colon	Sigmoid Colon
5	chr4:26863800-26870600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
6	chr4:26863800-26874600	Weak transcription	Left Ventricle	heart
7	chr4:26863800-26874600	Weak transcription	Spleen	Spleen
8	chr4:26863800-26875400	Weak transcription	Lung	lung
9	chr4:26864000-26867800	Weak transcription	Psoas Muscle	Psoas
10	chr4:26864200-26876800	Weak transcription	Colonic Mucosa	Colon
11	chr4:26864200-26877200	Weak transcription	Aorta	Aorta
12	chr4:26864400-26866800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr4:26864400-26869400	Weak transcription	Fetal Thymus	thymus
14	chr4:26864400-26869800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
15	chr4:26864400-26872600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
16	chr4:26864400-26873400	Weak transcription	A549	lung
17	chr4:26864400-26886600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr4:26864600-26866800	Weak transcription	Primary monocytes fromperipheralblood	blood
19	chr4:26864600-26866800	Weak transcription	Colon Smooth Muscle	Colon
20	chr4:26864600-26866800	Weak transcription	K562	blood
21	chr4:26864600-26867200	Enhancers	Brain Substantia Nigra	brain
22	chr4:26864600-26867200	Enhancers	Fetal Lung	lung
23	chr4:26864600-26867800	Weak transcription	Primary T cells fromperipheralblood	blood
24	chr4:26864600-26869200	Weak transcription	Fetal Kidney	kidney
25	chr4:26864600-26869400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr4:26864600-26869400	Weak transcription	Brain Germinal Matrix	brain
27	chr4:26864600-26869400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
28	chr4:26864600-26869600	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
29	chr4:26864600-26870800	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr4:26864600-26870800	Weak transcription	Fetal Muscle Trunk	muscle
31	chr4:26864600-26871000	Enhancers	Primary T regulatory cells fromperipheralblood	blood
32	chr4:26864600-26871800	Enhancers	Primary B cells from peripheral blood	blood
33	chr4:26864600-26872600	Weak transcription	Skeletal Muscle Female	skeletal muscle
34	chr4:26864600-26885600	Weak transcription	Thymus	Thymus
35	chr4:26864800-26866800	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr4:26864800-26867200	Enhancers	Primary hematopoietic stem cells short term culture	blood
37	chr4:26864800-26868000	Enhancers	HepG2	liver
38	chr4:26864800-26869200	Weak transcription	Fetal Heart	heart
39	chr4:26864800-26869400	Weak transcription	NH-A	brain
40	chr4:26864800-26871200	Enhancers	Primary T helper cells fromperipheralblood	blood
41	chr4:26864800-26872600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
42	chr4:26865000-26870600	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
43	chr4:26865200-26869400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr4:26865200-26873000	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr4:26865200-26873200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
46	chr4:26865400-26866800	Enhancers	HUVEC	blood vessel
47	chr4:26865400-26867000	Weak transcription	Right Atrium	heart
48	chr4:26865400-26867200	Enhancers	Brain Inferior Temporal Lobe	brain
49	chr4:26865400-26869400	Weak transcription	Fetal Muscle Leg	muscle
50	chr4:26865400-26869600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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