Variant report

Variant	rs7181399
Chromosome Location	chr15:57502703-57502704
allele	A/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	chr15:57502634-57502819	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57501438..57503633-chr15:57503718..57505515,2	MCF-7	breast:
2	chr15:57501824..57503369-chr15:57505657..57507843,2	K562	blood:

Variant related genes	Relation type
TCF12	TF binding region
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:39)

rs_ID	r²[population]
rs10467928	0.84[EUR][1000 genomes]
rs10467929	0.84[EUR][1000 genomes]
rs11071308	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs11853810	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs11856210	0.94[CEU][hapmap];0.93[EUR][1000 genomes]
rs16977278	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs16977306	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1841697	0.84[EUR][1000 genomes]
rs2414493	0.80[EUR][1000 genomes]
rs2591068	0.94[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.99[ASN][1000 genomes]
rs2593211	1.00[CEU][hapmap];0.84[EUR][1000 genomes]
rs2593249	0.84[CEU][hapmap];0.84[EUR][1000 genomes]
rs2593250	0.84[EUR][1000 genomes]
rs2703593	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.93[ASN][1000 genomes]
rs2703594	0.97[ASN][1000 genomes]
rs2703595	0.94[CEU][hapmap];0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs2733310	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.80[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2733334	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs28445470	0.82[EUR][1000 genomes]
rs28536671	0.81[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28653088	0.81[EUR][1000 genomes]
rs28781690	0.84[EUR][1000 genomes]
rs3803453	0.81[EUR][1000 genomes]
rs4774915	0.82[EUR][1000 genomes]
rs4774916	0.82[EUR][1000 genomes]
rs55742030	0.81[EUR][1000 genomes]
rs6493907	0.85[EUR][1000 genomes]
rs7163126	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7164298	0.82[CEU][hapmap]
rs7173477	0.82[EUR][1000 genomes]
rs7173748	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs7179311	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.90[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs720290	0.80[EUR][1000 genomes]
rs8024901	0.82[CEU][hapmap]
rs8026702	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs8034502	0.94[CEU][hapmap];0.84[EUR][1000 genomes]
rs8034744	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8034843	0.82[CEU][hapmap]
rs9672676	0.94[CEU][hapmap];1.00[CHB][hapmap];0.84[JPT][hapmap];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[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	nsv1042486	chr15:57094598-57505992	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
2	nsv904251	chr15:57241970-57575916	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	8 gene(s)	inside rSNPs	diseases
3	nsv1045611	chr15:57350965-58070807	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Active TSS ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv457164	chr15:57495060-57559387	Weak transcription Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
5	nsv569578	chr15:57495060-57559387	Enhancers Genic enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases
6	nsv833021	chr15:57495413-57751366	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7181399	LOC283663	Cis_1M	lymphoblastoid	RTeQTL
rs7181399	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:71 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57444400-57507400	Weak transcription	K562	blood
2	chr15:57453800-57524600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
3	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
4	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
5	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
7	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
9	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
10	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
11	chr15:57487200-57503000	Weak transcription	Liver	Liver
12	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
13	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:57490600-57505800	Weak transcription	NH-A	brain
17	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:57491000-57506000	Weak transcription	HMEC	breast
19	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:57491400-57503000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:57491400-57503000	Weak transcription	Primary T cells from cord blood	blood
22	chr15:57491400-57503200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
23	chr15:57491400-57505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
24	chr15:57491400-57505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:57491400-57506000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr15:57491400-57506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:57491400-57510000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
28	chr15:57491400-57510000	Weak transcription	Psoas Muscle	Psoas
29	chr15:57491400-57510200	Weak transcription	Monocytes-CD14+_RO01746	blood
30	chr15:57491400-57511200	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:57491600-57505200	Weak transcription	NHLF	lung
32	chr15:57491600-57506000	Weak transcription	Fetal Stomach	stomach
33	chr15:57491600-57508000	Weak transcription	HUVEC	blood vessel
34	chr15:57491600-57515200	Weak transcription	GM12878-XiMat	blood
35	chr15:57492000-57504200	Weak transcription	Brain Substantia Nigra	brain
36	chr15:57492000-57505200	Weak transcription	Fetal Kidney	kidney
37	chr15:57492400-57504200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr15:57492400-57504800	Weak transcription	Fetal Muscle Leg	muscle
39	chr15:57492400-57511600	Weak transcription	Left Ventricle	heart
40	chr15:57493600-57504800	Weak transcription	Brain Germinal Matrix	brain
41	chr15:57493600-57506000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr15:57494000-57504400	Weak transcription	HUES64 Cell Line	embryonic stem cell
43	chr15:57494000-57505400	Weak transcription	HSMM	muscle
44	chr15:57494000-57506000	Weak transcription	Fetal Intestine Large	intestine
45	chr15:57494000-57506000	Weak transcription	A549	lung
46	chr15:57494200-57505800	Weak transcription	HepG2	liver
47	chr15:57494200-57508600	Weak transcription	Dnd41	blood
48	chr15:57494400-57504400	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:57494800-57506200	Weak transcription	Duodenum Mucosa	Duodenum
50	chr15:57495000-57506000	Weak transcription	Stomach Mucosa	stomach

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