Variant report

Variant	rs13088856
Chromosome Location	chr3:159554958-159554959
allele	G/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	FOSL2	chr3:159554734-159555144	A549	lung:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
2	JUND	chr3:159554546-159555271	SK-N-SH	brain:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
3	STAT3	chr3:159554724-159555089	MCF10A-Er-Src	breast:	n/a	n/a
4	FOS	chr3:159554686-159555061	MCF10A-Er-Src	breast:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554839-159554850 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
5	GATA3	chr3:159554553-159555405	SK-N-SH	brain:	n/a	chr3:159555151-159555158 chr3:159555151-159555158 chr3:159554577-159554598 chr3:159555151-159555158 chr3:159555150-159555160 chr3:159555151-159555160 chr3:159555151-159555160
6	EP300	chr3:159554629-159555216	SK-N-SH_RA	brain:	n/a	chr3:159554840-159554849 chr3:159554936-159554950
7	STAT3	chr3:159554719-159555107	MCF10A-Er-Src	breast:	n/a	n/a
8	FOS	chr3:159554656-159555061	MCF10A-Er-Src	breast:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554839-159554850 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
9	MEF2A	chr3:159554443-159555214	SK-N-SH	brain:	n/a	chr3:159554855-159554864 chr3:159554841-159554849 chr3:159554850-159554871 chr3:159555032-159555040
10	POLR2A	chr3:159554547-159555290	HUVEC	blood vessel:	n/a	n/a
11	EP300	chr3:159554669-159555207	SK-N-SH_RA	brain:	n/a	chr3:159554840-159554849 chr3:159554936-159554950
12	MYC	chr3:159554753-159555061	MCF10A-Er-Src	breast:	n/a	n/a
13	FOS	chr3:159554687-159555060	MCF10A-Er-Src	breast:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554839-159554850 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
14	TCF12	chr3:159554531-159555405	SK-N-SH	brain:	n/a	n/a
15	STAT3	chr3:159554766-159555076	MCF10A-Er-Src	breast:	n/a	n/a
16	POLR2A	chr3:159554931-159554962	HUVEC	blood vessel:	n/a	n/a
17	PBX3	chr3:159554581-159555266	SK-N-SH	brain:	n/a	n/a
18	POLR2A	chr3:159554815-159555037	MCF10A-Er-Src	breast:	n/a	n/a
19	EP300	chr3:159554621-159555246	SK-N-SH	brain:	n/a	chr3:159554840-159554849 chr3:159554936-159554950
20	FOSL2	chr3:159554580-159555213	SK-N-SH	brain:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
21	FOS	chr3:159554656-159555045	MCF10A-Er-Src	breast:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554839-159554850 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
22	MYC	chr3:159554597-159555120	MCF10A-Er-Src	breast:	n/a	n/a
23	STAT3	chr3:159554714-159555094	MCF10A-Er-Src	breast:	n/a	n/a
24	TCF12	chr3:159554462-159555385	SK-N-SH	brain:	n/a	n/a
25	FOS	chr3:159554632-159555044	HUVEC	blood vessel:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554839-159554850 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
26	POLR2A	chr3:159554687-159555144	SK-N-SH	brain:	n/a	n/a
27	GATA3	chr3:159554570-159555325	SK-N-SH	brain:	n/a	chr3:159555151-159555158 chr3:159555151-159555158 chr3:159554577-159554598 chr3:159555151-159555158 chr3:159555150-159555160 chr3:159555151-159555160 chr3:159555151-159555160
28	MEF2A	chr3:159554680-159555233	SK-N-SH	brain:	n/a	chr3:159554855-159554864 chr3:159554841-159554849 chr3:159554850-159554871 chr3:159555032-159555040
29	JUND	chr3:159554538-159555221	SK-N-SH	brain:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849
30	PBX3	chr3:159554628-159555293	SK-N-SH	brain:	n/a	n/a
31	JUN	chr3:159554645-159555080	HUVEC	blood vessel:	n/a	chr3:159554841-159554849 chr3:159554837-159554848 chr3:159554840-159554850 chr3:159554841-159554849 chr3:159554840-159554850 chr3:159554842-159554849

Variant related genes	Relation type
SCHIP1	TF binding region

Extended variants
information (count: 5 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs10513546	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.91[TSI][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs13058787	0.81[CEU][hapmap]
rs13090881	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2169305	0.84[CEU][hapmap]
rs7648959	0.94[ASW][hapmap];1.00[CEU][hapmap];0.95[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.93[MEX][hapmap];0.99[MKK][hapmap];0.98[TSI][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13088856	IL12A	cis	parietal	SCAN

Chromatin state (count:64 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:159543600-159555200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:159543800-159555200	Weak transcription	Lung	lung
3	chr3:159547000-159557400	Weak transcription	Fetal Kidney	kidney
4	chr3:159547800-159556800	Weak transcription	Brain Germinal Matrix	brain
5	chr3:159548600-159555000	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr3:159548600-159555200	Weak transcription	Left Ventricle	heart
7	chr3:159549000-159555000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
8	chr3:159549000-159555200	Weak transcription	Right Atrium	heart
9	chr3:159549000-159555200	Weak transcription	Right Ventricle	heart
10	chr3:159549000-159555600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
11	chr3:159550000-159555000	Weak transcription	Fetal Muscle Leg	muscle
12	chr3:159550200-159557600	Weak transcription	Primary B cells from cord blood	blood
13	chr3:159550200-159557600	Weak transcription	Spleen	Spleen
14	chr3:159550600-159555600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr3:159551400-159561800	Weak transcription	Aorta	Aorta
16	chr3:159551800-159557600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
17	chr3:159551800-159557600	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr3:159552800-159557400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr3:159552800-159557800	Enhancers	HUVEC	blood vessel
20	chr3:159553000-159556200	Enhancers	Colon Smooth Muscle	Colon
21	chr3:159553200-159557400	Enhancers	Rectal Smooth Muscle	rectum
22	chr3:159553600-159556000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr3:159553600-159556000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr3:159553600-159556000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
25	chr3:159553600-159556000	Enhancers	NHDF-Ad	bronchial
26	chr3:159553800-159555800	Enhancers	Fetal Heart	heart
27	chr3:159553800-159556000	Enhancers	Brain Cingulate Gyrus	brain
28	chr3:159553800-159556000	Enhancers	HSMMtube	muscle
29	chr3:159554000-159555800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr3:159554000-159556000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr3:159554000-159556000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr3:159554000-159556000	Enhancers	Duodenum Smooth Muscle	Duodenum
33	chr3:159554000-159556000	Enhancers	Fetal Stomach	stomach
34	chr3:159554000-159556000	Enhancers	Skeletal Muscle Male	skeletal muscle
35	chr3:159554000-159556000	Enhancers	Stomach Smooth Muscle	stomach
36	chr3:159554000-159556000	Enhancers	HSMM	muscle
37	chr3:159554000-159557200	Enhancers	Brain Angular Gyrus	brain
38	chr3:159554000-159557400	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr3:159554000-159557400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
40	chr3:159554000-159557400	Enhancers	Brain Hippocampus Middle	brain
41	chr3:159554000-159557400	Enhancers	Brain Substantia Nigra	brain
42	chr3:159554200-159555400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
43	chr3:159554200-159555800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr3:159554200-159555800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr3:159554200-159555800	Enhancers	Muscle Satellite Cultured Cells	--
46	chr3:159554200-159555800	Enhancers	Adipose Nuclei	Adipose
47	chr3:159554200-159555800	Enhancers	NH-A	brain
48	chr3:159554200-159555800	Enhancers	Osteobl	bone
49	chr3:159554200-159556000	Enhancers	Brain Inferior Temporal Lobe	brain
50	chr3:159554200-159556000	Enhancers	Hela-S3	cervix

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