Variant report

Variant	rs13313455
Chromosome Location	chr15:57408980-57408981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:136)

rs_ID	r²[population]
rs1037956	0.85[CHB][hapmap];0.95[JPT][hapmap]
rs1037958	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs10518894	0.90[CHB][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs10518895	0.85[CHB][hapmap];0.91[JPT][hapmap];0.83[ASN][1000 genomes]
rs11071309	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11630195	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs11631541	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11632069	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11635440	0.91[JPT][hapmap]
rs11635645	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11636100	0.89[ASN][1000 genomes]
rs11637955	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs11852340	0.90[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]
rs11853331	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11855648	0.85[CHB][hapmap];0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs11857507	0.95[JPT][hapmap]
rs11858471	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs11858783	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12898327	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12899036	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12899187	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs12899904	0.84[ASN][1000 genomes]
rs12899915	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs12900038	0.84[ASN][1000 genomes]
rs12900589	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[EUR][1000 genomes]
rs12900874	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.81[EUR][1000 genomes]
rs12900986	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12902058	0.83[YRI][hapmap]
rs12904634	0.91[JPT][hapmap]
rs12904933	0.91[JPT][hapmap]
rs12905900	0.89[CHB][hapmap];0.86[JPT][hapmap]
rs12906025	0.82[YRI][hapmap]
rs12906042	0.83[CHB][hapmap];0.94[JPT][hapmap]
rs12906873	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs12909402	0.87[ASN][1000 genomes]
rs12910094	0.85[CHB][hapmap];0.86[JPT][hapmap];0.82[ASN][1000 genomes]
rs12910170	0.87[ASN][1000 genomes]
rs12912007	0.84[ASN][1000 genomes]
rs12912210	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs12912868	0.91[JPT][hapmap]
rs12914182	0.82[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12914425	0.84[CHB][hapmap];0.90[JPT][hapmap]
rs12915489	0.83[CHB][hapmap];0.83[JPT][hapmap]
rs12916237	0.82[CEU][hapmap];0.83[CHB][hapmap];0.85[JPT][hapmap]
rs12916958	0.85[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap]
rs12917247	0.89[CHB][hapmap];0.91[JPT][hapmap]
rs1430823	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs1545728	0.85[JPT][hapmap]
rs1628067	0.92[CEU][hapmap];0.89[CHB][hapmap];0.90[JPT][hapmap]
rs17239040	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs17239508	0.84[CHB][hapmap];0.91[JPT][hapmap]
rs17819700	0.82[CEU][hapmap];0.85[CHB][hapmap];0.87[JPT][hapmap]
rs1814585	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs1820995	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs1867641	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2111890	0.82[YRI][hapmap]
rs213149	0.92[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs2169465	0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2169466	0.90[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2264904	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2290938	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs2414490	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs2414491	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2414492	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs2435907	0.83[EUR][1000 genomes]
rs2439918	0.84[EUR][1000 genomes]
rs2439919	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2464429	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2464430	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2470079	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2470082	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2585082	0.86[JPT][hapmap]
rs2585087	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2585088	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2585102	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2585112	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2615231	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2703576	1.00[CEU][hapmap];1.00[CHB][hapmap];0.91[JPT][hapmap];0.85[EUR][1000 genomes]
rs2703577	0.85[EUR][1000 genomes]
rs2703580	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.85[EUR][1000 genomes]
rs2733170	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.81[EUR][1000 genomes]
rs2733171	0.89[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap]
rs2733174	0.89[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap]
rs2733177	0.84[EUR][1000 genomes]
rs2733182	0.83[EUR][1000 genomes]
rs2733185	0.84[EUR][1000 genomes]
rs2733188	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2733307	0.89[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2733332	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28414972	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28514688	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28648502	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920265	0.83[EUR][1000 genomes]
rs2920267	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2920269	0.83[EUR][1000 genomes]
rs2927189	0.81[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951895	0.81[EUR][1000 genomes]
rs2951898	0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2951899	0.96[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.85[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2951901	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2951903	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[EUR][1000 genomes]
rs2951904	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes]
rs2951906	0.83[EUR][1000 genomes]
rs2957574	0.83[EUR][1000 genomes]
rs2957591	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962990	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes]
rs2962991	0.96[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.84[EUR][1000 genomes]
rs2962992	0.92[CEU][hapmap];0.90[CHB][hapmap];0.90[JPT][hapmap];0.84[EUR][1000 genomes]
rs2962993	0.89[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap]
rs3095821	0.91[JPT][hapmap]
rs34262415	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs3794613	0.91[JPT][hapmap]
rs3803454	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs3803455	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs4238321	0.84[CHB][hapmap];0.86[JPT][hapmap]
rs4353440	0.84[CHB][hapmap];0.84[JPT][hapmap]
rs4774246	0.81[YRI][hapmap]
rs4774250	0.80[CHB][hapmap]
rs4774902	0.85[CHB][hapmap];0.87[JPT][hapmap]
rs4774910	0.83[CEU][hapmap];0.90[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4774913	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs6493901	0.82[CEU][hapmap];0.89[CHB][hapmap];0.91[JPT][hapmap];0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs715338	0.85[CHB][hapmap];0.86[JPT][hapmap]
rs7161965	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7168387	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7168945	0.82[YRI][hapmap]
rs7173936	0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs7175436	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap]
rs745652	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs7496293	0.84[CHB][hapmap];0.87[JPT][hapmap]
rs8023343	0.82[YRI][hapmap]
rs8035485	0.81[YRI][hapmap]
rs8037901	0.85[CEU][hapmap];0.85[CHB][hapmap];0.91[JPT][hapmap];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs935326	0.85[CHB][hapmap];0.91[JPT][hapmap]
rs967514	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs978274	0.85[CHB][hapmap];0.91[JPT][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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs13313455	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57372800-57410200	Weak transcription	Muscle Satellite Cultured Cells	--
2	chr15:57374800-57409600	Weak transcription	Osteobl	bone
3	chr15:57374800-57414600	Weak transcription	Fetal Kidney	kidney
4	chr15:57381000-57412400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr15:57381200-57409400	Weak transcription	NHLF	lung
6	chr15:57382600-57423800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
7	chr15:57382800-57419600	Weak transcription	K562	blood
8	chr15:57384200-57409200	Weak transcription	Brain Germinal Matrix	brain
9	chr15:57384600-57410400	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
10	chr15:57386200-57410200	Weak transcription	Ovary	ovary
11	chr15:57386400-57426600	Weak transcription	Primary T cells fromperipheralblood	blood
12	chr15:57386600-57424600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
14	chr15:57387200-57425400	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr15:57387600-57409400	Weak transcription	Dnd41	blood
16	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
17	chr15:57390200-57409400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
18	chr15:57391200-57410200	Weak transcription	HMEC	breast
19	chr15:57391400-57409600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
20	chr15:57397800-57416600	Weak transcription	Fetal Stomach	stomach
21	chr15:57398000-57415800	Weak transcription	Fetal Intestine Small	intestine
22	chr15:57399400-57409200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
23	chr15:57399400-57409600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
24	chr15:57399400-57410000	Weak transcription	NH-A	brain
25	chr15:57399400-57424600	Weak transcription	Primary T helper cells PMA-I stimulated	--
26	chr15:57399600-57410000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:57399600-57410200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr15:57399600-57416200	Weak transcription	Primary T cells from cord blood	blood
29	chr15:57401600-57410200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr15:57402000-57410200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
31	chr15:57402600-57414600	Weak transcription	Primary B cells from cord blood	blood
32	chr15:57403000-57424600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
33	chr15:57403800-57425200	Weak transcription	H9 Cell Line	embryonic stem cell
34	chr15:57404600-57409400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr15:57404600-57409800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
36	chr15:57404600-57410200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:57404600-57410200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
38	chr15:57404600-57425000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
39	chr15:57404800-57409400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr15:57404800-57409800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:57404800-57410200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:57404800-57410200	Weak transcription	H1 Cell Line	embryonic stem cell
43	chr15:57404800-57410200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
44	chr15:57404800-57410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:57404800-57410200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
46	chr15:57404800-57410200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr15:57404800-57410200	Strong transcription	Fetal Thymus	thymus
48	chr15:57404800-57410200	Weak transcription	Skeletal Muscle Male	skeletal muscle
49	chr15:57404800-57410200	Weak transcription	HSMM	muscle
50	chr15:57404800-57410200	Weak transcription	NHEK	skin

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