Variant report

Variant	rs28756149
Chromosome Location	chr15:57248242-57248243
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 50 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs11071303	0.85[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11856411	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12324092	0.82[EUR][1000 genomes]
rs12901355	0.84[EUR][1000 genomes]
rs1430820	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1430822	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs16977153	0.88[ASN][1000 genomes]
rs16977222	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs17415731	0.95[ASN][1000 genomes]
rs1820994	0.82[ASN][1000 genomes]
rs28360967	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28422021	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28505122	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs28533433	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs28541606	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs28612876	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28616268	0.85[EUR][1000 genomes]
rs28648577	0.85[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28649108	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28654848	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28677775	0.94[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28814080	0.94[AFR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28856894	0.95[EUR][1000 genomes]
rs4774245	0.87[ASN][1000 genomes]
rs67149912	0.84[EUR][1000 genomes]
rs7162194	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7164655	0.93[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7169053	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7171073	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs7171304	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs7176873	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs7178030	0.80[EUR][1000 genomes]
rs7178833	0.86[ASN][1000 genomes]
rs8023343	0.82[ASN][1000 genomes]
rs8023816	0.85[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8031516	0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8031640	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8032615	0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs8033010	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8034066	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8035485	0.91[ASN][1000 genomes]
rs8039899	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8040708	0.95[EUR][1000 genomes]
rs9302200	0.84[EUR][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	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv904250	chr15:57225766-57294085	ZNF genes & repeats Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	3 gene(s)	inside rSNPs	diseases
4	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	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

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs28756149	TCF12	Cis_1M	lymphoblastoid	RTeQTL
rs28756149	LOC283663	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57212400-57256000	Weak transcription	Pancreas	Pancrea
2	chr15:57213200-57256000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:57222600-57250200	Weak transcription	NH-A	brain
4	chr15:57222800-57255000	Weak transcription	HMEC	breast
5	chr15:57224600-57248600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
6	chr15:57225000-57249000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr15:57227000-57249800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
8	chr15:57227600-57260600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr15:57228200-57260600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
10	chr15:57229400-57255800	Weak transcription	Fetal Stomach	stomach
11	chr15:57232000-57256000	Weak transcription	Skeletal Muscle Male	skeletal muscle
12	chr15:57233000-57250200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:57234400-57249000	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:57236800-57249800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
15	chr15:57238200-57249000	Weak transcription	HSMM	muscle
16	chr15:57238400-57249000	Weak transcription	Primary hematopoietic stem cells	blood
17	chr15:57238400-57256200	Weak transcription	K562	blood
18	chr15:57239600-57250200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:57240200-57249200	Weak transcription	Psoas Muscle	Psoas
20	chr15:57240200-57250200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
21	chr15:57240200-57250200	Weak transcription	Left Ventricle	heart
22	chr15:57241000-57249000	Weak transcription	HUES48 Cell Line	embryonic stem cell
23	chr15:57241000-57255600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:57241200-57251600	Weak transcription	Brain Inferior Temporal Lobe	brain
25	chr15:57241200-57254400	Weak transcription	NHLF	lung
26	chr15:57241600-57249200	Weak transcription	Osteobl	bone
27	chr15:57242200-57249800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
28	chr15:57242200-57251400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
29	chr15:57242200-57256000	Weak transcription	Ovary	ovary
30	chr15:57242400-57249200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
31	chr15:57242400-57250000	Weak transcription	Thymus	Thymus
32	chr15:57242600-57252000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr15:57244000-57255800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
34	chr15:57244200-57249200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
35	chr15:57244200-57249200	Weak transcription	Dnd41	blood
36	chr15:57244200-57257800	Weak transcription	Fetal Intestine Small	intestine
37	chr15:57246800-57249200	Weak transcription	Fetal Thymus	thymus
38	chr15:57246800-57256000	Weak transcription	Gastric	stomach
39	chr15:57247000-57249400	ZNF genes & repeats	Fetal Lung	lung
40	chr15:57248200-57248400	Enhancers	HUES64 Cell Line	embryonic stem cell
41	chr15:57248200-57249800	Enhancers	HepG2	liver
42	chr15:57248200-57250800	Enhancers	iPS-20b Cell Line	embryonic stem cell

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