Variant report

Variant	rs7179311
Chromosome Location	chr15:57493955-57493956
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57489296..57493196-chr15:57493593..57496438,4	K562	blood:
2	chr15:57489288..57492189-chr15:57492368..57494008,2	MCF-7	breast:
3	chr15:57491334..57495003-chr15:57497716..57500211,4	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs10467928	0.85[EUR][1000 genomes]
rs10467929	0.85[EUR][1000 genomes]
rs11071308	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs11853810	0.88[CEU][hapmap]
rs11856210	0.94[CEU][hapmap];0.94[EUR][1000 genomes]
rs16977278	0.94[CEU][hapmap];0.95[EUR][1000 genomes]
rs16977306	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16977374	0.81[CEU][hapmap]
rs1841697	0.85[EUR][1000 genomes]
rs2591068	0.94[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.80[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2593211	1.00[CEU][hapmap];0.85[EUR][1000 genomes]
rs2593249	0.89[CEU][hapmap];0.85[EUR][1000 genomes]
rs2593250	0.85[EUR][1000 genomes]
rs2703593	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2703594	0.98[ASN][1000 genomes]
rs2703595	0.94[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap];0.80[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733310	0.88[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs2733334	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs28536671	0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28781690	0.85[EUR][1000 genomes]
rs3803453	0.81[CEU][hapmap]
rs6493907	0.82[EUR][1000 genomes]
rs7163126	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7164298	0.87[CEU][hapmap]
rs7173748	0.92[CEU][hapmap];0.95[EUR][1000 genomes]
rs7180558	0.81[CEU][hapmap]
rs7181399	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]
rs8024901	0.87[CEU][hapmap]
rs8026702	0.94[CEU][hapmap];0.96[EUR][1000 genomes]
rs8033118	0.82[AFR][1000 genomes]
rs8034502	0.94[CEU][hapmap];0.85[EUR][1000 genomes]
rs8034744	1.00[CEU][hapmap];1.00[CHB][hapmap];0.90[JPT][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs8034843	0.88[CEU][hapmap]
rs9672676	0.94[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs997683	0.82[CEU][hapmap]

Variant overlapped rSNPs/rCNVs (count:3 , 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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7179311	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs7179311	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:88 , 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	chr15:57457200-57499400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
4	chr15:57458200-57505200	Strong transcription	Fetal Thymus	thymus
5	chr15:57478600-57494000	Weak transcription	Pancreas	Pancrea
6	chr15:57478800-57526200	Weak transcription	Hela-S3	cervix
7	chr15:57479400-57524800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr15:57481800-57524600	Weak transcription	Right Ventricle	heart
9	chr15:57484800-57496200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr15:57484800-57502000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
11	chr15:57485000-57501000	Weak transcription	Spleen	Spleen
12	chr15:57485000-57501800	Weak transcription	Lung	lung
13	chr15:57485000-57506200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
14	chr15:57485600-57505000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
15	chr15:57486600-57496000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr15:57486800-57505800	Weak transcription	NHDF-Ad	bronchial
17	chr15:57487000-57496600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
18	chr15:57487000-57524400	Weak transcription	Placenta	Placenta
19	chr15:57487200-57503000	Weak transcription	Liver	Liver
20	chr15:57487200-57511200	Weak transcription	Fetal Muscle Trunk	muscle
21	chr15:57488200-57511600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:57488400-57494000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:57488400-57496000	Weak transcription	Primary hematopoietic stem cells	blood
24	chr15:57488400-57496000	Weak transcription	Fetal Intestine Small	intestine
25	chr15:57489200-57496000	Weak transcription	Osteobl	bone
26	chr15:57489200-57506000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr15:57489400-57506200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:57489800-57494200	Strong transcription	Dnd41	blood
29	chr15:57490200-57494400	Enhancers	Brain Hippocampus Middle	brain
30	chr15:57490600-57505800	Weak transcription	NH-A	brain
31	chr15:57490800-57496400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:57491000-57495000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
33	chr15:57491000-57501400	Weak transcription	Primary T helper cells fromperipheralblood	blood
34	chr15:57491000-57505600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
35	chr15:57491000-57506000	Weak transcription	HMEC	breast
36	chr15:57491200-57508000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
37	chr15:57491400-57494200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr15:57491400-57496000	Weak transcription	Ovary	ovary
39	chr15:57491400-57497200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
40	chr15:57491400-57497200	Weak transcription	Right Atrium	heart
41	chr15:57491400-57497800	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
42	chr15:57491400-57500800	Weak transcription	Thymus	Thymus
43	chr15:57491400-57501200	Weak transcription	Primary B cells from cord blood	blood
44	chr15:57491400-57503000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
45	chr15:57491400-57503000	Weak transcription	Primary T cells from cord blood	blood
46	chr15:57491400-57503200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:57491400-57505800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr15:57491400-57505800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr15:57491400-57506000	Weak transcription	Primary monocytes fromperipheralblood	blood
50	chr15:57491400-57506200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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