Variant report

Variant	rs28514688
Chromosome Location	chr15:57399988-57399989
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57397844..57400555-chr15:57402758..57405029,3	K562	blood:

Extended variants
information (count: 74 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:71)

rs_ID	r²[population]
rs10467927	0.85[AFR][1000 genomes]
rs10518894	0.86[ASN][1000 genomes]
rs10518895	0.81[ASN][1000 genomes]
rs11071305	0.81[ASN][1000 genomes]
rs11635645	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11636100	0.88[ASN][1000 genomes]
rs11852340	0.88[ASN][1000 genomes]
rs11855648	0.84[ASN][1000 genomes]
rs12591430	0.82[AFR][1000 genomes]
rs12899904	0.83[ASN][1000 genomes]
rs12900038	0.83[ASN][1000 genomes]
rs12900589	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs12900874	0.81[EUR][1000 genomes]
rs12909402	0.89[ASN][1000 genomes]
rs12910170	0.90[ASN][1000 genomes]
rs12912007	0.83[ASN][1000 genomes]
rs12914182	0.81[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs13313455	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs13379847	0.83[AFR][1000 genomes]
rs1820995	0.83[EUR][1000 genomes]
rs2169465	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2169466	0.87[ASN][1000 genomes]
rs2264904	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2435907	0.83[EUR][1000 genomes]
rs2439918	0.84[EUR][1000 genomes]
rs2439919	0.81[AFR][1000 genomes];0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2464429	0.84[EUR][1000 genomes]
rs2464430	0.84[EUR][1000 genomes]
rs2470079	0.81[EUR][1000 genomes]
rs2470082	0.80[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs2585088	0.83[EUR][1000 genomes]
rs2585112	0.84[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2615231	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2703576	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2703577	0.85[EUR][1000 genomes]
rs2703580	0.85[EUR][1000 genomes]
rs2733170	0.81[EUR][1000 genomes]
rs2733177	0.84[EUR][1000 genomes]
rs2733182	0.83[EUR][1000 genomes]
rs2733185	0.84[EUR][1000 genomes]
rs2733188	0.91[AFR][1000 genomes];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2733307	0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733332	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28414972	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs28648502	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs28712697	0.81[AFR][1000 genomes]
rs2920265	0.83[EUR][1000 genomes]
rs2920267	0.84[EUR][1000 genomes]
rs2920269	0.83[EUR][1000 genomes]
rs2927189	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951895	0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2951898	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2951899	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2951901	0.83[EUR][1000 genomes]
rs2951903	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2951904	0.84[EUR][1000 genomes]
rs2951906	0.83[EUR][1000 genomes]
rs2957574	0.83[EUR][1000 genomes]
rs2957591	0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2962990	0.83[EUR][1000 genomes]
rs2962991	0.84[EUR][1000 genomes]
rs2962992	0.84[EUR][1000 genomes]
rs4774910	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493901	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs67077316	0.86[AFR][1000 genomes]
rs7168387	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7173936	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs8037901	0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs967514	0.86[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9806170	0.80[AFR][1000 genomes]
rs9806199	0.80[AFR][1000 genomes]

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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs28514688	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:80 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
3	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
4	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
5	chr15:57374800-57409600	Weak transcription	Osteobl	bone
6	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
7	chr15:57376200-57406000	Weak transcription	Rectal Mucosa Donor 31	rectum
8	chr15:57380200-57401000	Strong transcription	Fetal Thymus	thymus
9	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
10	chr15:57381200-57404400	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr15:57381200-57409400	Weak transcription	NHLF	lung
12	chr15:57381800-57403200	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr15:57382600-57403400	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:57382600-57403800	Weak transcription	Left Ventricle	heart
15	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr15:57382800-57404400	Weak transcription	Brain Inferior Temporal Lobe	brain
17	chr15:57382800-57404400	Weak transcription	Stomach Smooth Muscle	stomach
18	chr15:57382800-57419600	Weak transcription	K562	blood
19	chr15:57383000-57404000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:57383200-57403200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
21	chr15:57384200-57409200	Weak transcription	Brain Germinal Matrix	brain
22	chr15:57384600-57401400	Weak transcription	Brain Angular Gyrus	brain
23	chr15:57384600-57404400	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
24	chr15:57384600-57405600	Weak transcription	Brain Anterior Caudate	brain
25	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
26	chr15:57385200-57406200	Weak transcription	HepG2	liver
27	chr15:57386200-57410200	Weak transcription	Ovary	ovary
28	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
29	chr15:57386600-57404000	Weak transcription	HUES64 Cell Line	embryonic stem cell
30	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr15:57386800-57405600	Weak transcription	HUES48 Cell Line	embryonic stem cell
32	chr15:57387000-57404400	Weak transcription	Duodenum Smooth Muscle	Duodenum
33	chr15:57387000-57406400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
34	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
35	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
36	chr15:57387400-57403800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr15:57387400-57406000	Weak transcription	Duodenum Mucosa	Duodenum
38	chr15:57387400-57406200	Weak transcription	HUVEC	blood vessel
39	chr15:57387600-57409400	Weak transcription	Dnd41	blood
40	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
41	chr15:57387800-57401200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
42	chr15:57388000-57404200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
43	chr15:57388200-57406200	Weak transcription	A549	lung
44	chr15:57389000-57404400	Weak transcription	HSMM	muscle
45	chr15:57390200-57409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr15:57391200-57404400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
47	chr15:57391200-57410200	Weak transcription	HMEC	breast
48	chr15:57391400-57409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr15:57391800-57404400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
50	chr15:57392400-57402800	Weak transcription	Brain Hippocampus Middle	brain

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