Variant report

Variant	rs12914410
Chromosome Location	chr15:57429837-57429838
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:57408243..57410631-chr15:57428939..57431459,2	K562	blood:
2	chr15:57422589..57424101-chr15:57429055..57431848,2	K562	blood:
3	chr15:57428236..57433536-chr15:57434011..57440588,9	K562	blood:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction

Extended variants
information (count: 95 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:92)

rs_ID	r²[population]
rs10518894	0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs10518895	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs10518899	0.83[EUR][1000 genomes]
rs11071305	0.91[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11071309	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs11630195	0.84[AMR][1000 genomes]
rs11631228	0.82[AMR][1000 genomes]
rs11631541	0.83[AMR][1000 genomes]
rs11632069	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11633061	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11635645	0.85[ASN][1000 genomes]
rs11636100	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11636201	0.85[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11636348	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs11636919	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs11852340	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11853331	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11855648	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11858783	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12050751	0.82[EUR][1000 genomes]
rs12050758	0.82[EUR][1000 genomes]
rs12898327	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12898844	0.83[EUR][1000 genomes]
rs12899036	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs12899187	0.82[AMR][1000 genomes]
rs12899588	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12899904	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12899915	0.84[AMR][1000 genomes]
rs12900038	0.83[AFR][1000 genomes];0.86[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12900986	0.82[AMR][1000 genomes]
rs12901780	0.82[AMR][1000 genomes]
rs12903115	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12903578	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12904321	0.82[EUR][1000 genomes]
rs12904501	0.82[EUR][1000 genomes]
rs12904602	0.80[EUR][1000 genomes]
rs12905900	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12906042	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12906335	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12906873	0.84[AMR][1000 genomes]
rs12906936	0.84[AMR][1000 genomes]
rs12908760	0.82[EUR][1000 genomes]
rs12909402	0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12909811	0.82[AMR][1000 genomes]
rs12910094	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12910170	0.80[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12910556	0.80[EUR][1000 genomes]
rs12910832	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12911518	0.82[EUR][1000 genomes]
rs12912007	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12912210	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12914182	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914425	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914481	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12915473	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12916237	0.82[AMR][1000 genomes]
rs12916478	0.82[EUR][1000 genomes]
rs12916958	0.82[AMR][1000 genomes]
rs12917247	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs1430823	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs1462156	0.82[EUR][1000 genomes]
rs17239040	0.84[AMR][1000 genomes]
rs1814585	0.82[EUR][1000 genomes]
rs2111891	0.84[AMR][1000 genomes]
rs2116065	0.82[AMR][1000 genomes]
rs2116066	0.82[AMR][1000 genomes]
rs2169465	0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2169466	0.86[ASN][1000 genomes]
rs2414491	0.83[AMR][1000 genomes];0.85[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2414494	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2414497	0.80[EUR][1000 genomes]
rs2583108	0.80[AMR][1000 genomes]
rs2585087	0.81[AMR][1000 genomes]
rs2593237	0.82[EUR][1000 genomes]
rs2593238	0.83[EUR][1000 genomes]
rs2733171	0.81[AMR][1000 genomes]
rs2733176	0.82[AMR][1000 genomes]
rs2733307	0.85[ASN][1000 genomes]
rs2733341	0.80[ASN][1000 genomes]
rs28648502	0.80[ASN][1000 genomes]
rs34262415	0.82[AMR][1000 genomes]
rs35646942	0.82[AMR][1000 genomes]
rs3803454	0.82[AMR][1000 genomes]
rs4774250	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs4774910	0.85[AFR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4774913	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs62022986	0.82[AMR][1000 genomes]
rs62022988	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs6493901	0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7161965	0.82[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs745652	0.86[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs8037901	0.82[EUR][1000 genomes];0.88[ASN][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
rs12914410	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57387000-57430000	Weak transcription	Placenta	Placenta
2	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
3	chr15:57410600-57440800	Weak transcription	Ovary	ovary
4	chr15:57411000-57430400	Weak transcription	NH-A	brain
5	chr15:57415000-57438800	Weak transcription	Primary monocytes fromperipheralblood	blood
6	chr15:57415600-57438800	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr15:57416000-57438800	Weak transcription	Primary B cells from cord blood	blood
8	chr15:57416800-57430800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr15:57419600-57439000	Weak transcription	Fetal Intestine Small	intestine
10	chr15:57421800-57436600	Weak transcription	Primary neutrophils fromperipheralblood	blood
11	chr15:57422600-57430400	Weak transcription	Fetal Heart	heart
12	chr15:57425600-57432200	Enhancers	Fetal Lung	lung
13	chr15:57425800-57430400	Weak transcription	Right Atrium	heart
14	chr15:57425800-57430400	Weak transcription	Skeletal Muscle Male	skeletal muscle
15	chr15:57425800-57434800	Strong transcription	Fetal Thymus	thymus
16	chr15:57425800-57438800	Weak transcription	HSMM	muscle
17	chr15:57425800-57440800	Weak transcription	Thymus	Thymus
18	chr15:57425800-57442200	Weak transcription	Right Ventricle	heart
19	chr15:57426000-57431000	Enhancers	Brain Hippocampus Middle	brain
20	chr15:57426000-57431800	Enhancers	Brain Substantia Nigra	brain
21	chr15:57426200-57432400	Enhancers	Brain Cingulate Gyrus	brain
22	chr15:57426800-57430600	Weak transcription	Small Intestine	intestine
23	chr15:57426800-57436200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr15:57426800-57438400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr15:57427200-57440000	Weak transcription	Fetal Stomach	stomach
26	chr15:57427400-57430000	Weak transcription	H1 Cell Line	embryonic stem cell
27	chr15:57427400-57430400	Weak transcription	H9 Cell Line	embryonic stem cell
28	chr15:57427400-57432600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
29	chr15:57427400-57436200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
30	chr15:57427400-57439000	Weak transcription	A549	lung
31	chr15:57427400-57442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
32	chr15:57427600-57440600	Weak transcription	Dnd41	blood
33	chr15:57427800-57430200	Weak transcription	HUES6 Cell Line	embryonic stem cell
34	chr15:57428000-57430000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:57428200-57432600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
36	chr15:57428200-57437800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
37	chr15:57428400-57430200	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:57428400-57430200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
39	chr15:57428400-57430400	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:57428400-57430400	Weak transcription	Fetal Brain Male	brain
41	chr15:57428400-57434600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
42	chr15:57428400-57438800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
43	chr15:57428400-57442200	Weak transcription	Primary T cells from cord blood	blood
44	chr15:57428600-57430200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
45	chr15:57428600-57430200	Weak transcription	HUES64 Cell Line	embryonic stem cell
46	chr15:57428600-57430200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr15:57428600-57430400	Weak transcription	Brain Angular Gyrus	brain
48	chr15:57428600-57435600	Weak transcription	Osteobl	bone
49	chr15:57428600-57436200	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
50	chr15:57428600-57438000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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