Variant report

Variant	rs2414494
Chromosome Location	chr15:57441738-57441739
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 108 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:105)

rs_ID	r²[population]
rs1037956	0.81[EUR][1000 genomes]
rs1037958	0.81[EUR][1000 genomes]
rs10518894	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10518895	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10518899	0.85[EUR][1000 genomes]
rs11071305	0.90[EUR][1000 genomes]
rs11071309	0.83[EUR][1000 genomes]
rs11630195	0.85[AMR][1000 genomes]
rs11631228	0.83[AMR][1000 genomes]
rs11631541	0.84[AMR][1000 genomes]
rs11632069	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11633061	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs11635645	0.82[ASN][1000 genomes]
rs11636100	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11636201	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636348	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11636919	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11637955	0.82[EUR][1000 genomes]
rs11852340	0.82[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11853331	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11855648	0.80[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11856055	0.80[EUR][1000 genomes]
rs11858783	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12050751	0.85[EUR][1000 genomes]
rs12050758	0.85[EUR][1000 genomes]
rs12898327	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12898356	0.82[EUR][1000 genomes]
rs12898844	0.81[EUR][1000 genomes]
rs12899036	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12899187	0.83[AMR][1000 genomes]
rs12899588	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899904	0.89[AFR][1000 genomes];0.84[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12899915	0.85[AMR][1000 genomes]
rs12900038	0.84[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12900986	0.83[AMR][1000 genomes]
rs12901671	0.81[EUR][1000 genomes]
rs12901780	0.83[AMR][1000 genomes]
rs12902170	0.81[EUR][1000 genomes]
rs12903115	0.86[EUR][1000 genomes]
rs12903578	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12904321	0.85[EUR][1000 genomes]
rs12904501	0.85[EUR][1000 genomes]
rs12904602	0.83[EUR][1000 genomes]
rs12905900	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12906042	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12906335	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12906566	0.81[EUR][1000 genomes]
rs12906873	0.85[AMR][1000 genomes]
rs12906936	0.85[AMR][1000 genomes]
rs12908760	0.85[EUR][1000 genomes]
rs12909016	0.81[EUR][1000 genomes]
rs12909402	0.82[ASN][1000 genomes]
rs12909811	0.83[AMR][1000 genomes]
rs12910094	0.84[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12910170	0.82[ASN][1000 genomes]
rs12910556	0.83[EUR][1000 genomes]
rs12910832	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12911518	0.84[EUR][1000 genomes]
rs12912007	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12912210	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs12912353	0.81[EUR][1000 genomes]
rs12912392	0.82[EUR][1000 genomes]
rs12914182	0.84[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12914410	0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12914425	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12914481	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12915473	0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12916237	0.83[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12916478	0.84[EUR][1000 genomes]
rs12916958	0.83[AMR][1000 genomes]
rs12917093	0.81[EUR][1000 genomes]
rs12917247	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1430823	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs1462156	0.84[EUR][1000 genomes]
rs17239040	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs17239431	0.82[EUR][1000 genomes]
rs1814585	0.85[EUR][1000 genomes]
rs1867641	0.82[EUR][1000 genomes]
rs2116065	0.83[AMR][1000 genomes]
rs2116066	0.83[AMR][1000 genomes]
rs2169465	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2169466	0.82[ASN][1000 genomes]
rs2290938	0.81[EUR][1000 genomes]
rs2414491	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2414497	0.83[EUR][1000 genomes]
rs2583108	0.81[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs2585087	0.82[AMR][1000 genomes]
rs2593237	0.85[EUR][1000 genomes]
rs2593238	0.85[EUR][1000 genomes]
rs2733171	0.82[AMR][1000 genomes]
rs2733174	0.80[AMR][1000 genomes]
rs2733176	0.83[AMR][1000 genomes]
rs2733307	0.82[ASN][1000 genomes]
rs34262415	0.83[AMR][1000 genomes]
rs35646942	0.83[AMR][1000 genomes]
rs4774250	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4774910	0.80[AFR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4774913	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62022986	0.83[AMR][1000 genomes]
rs62022988	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493901	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7161965	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs745652	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs8037901	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs978274	0.82[EUR][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
rs2414494	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:93 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57387600-57442400	Weak transcription	Fetal Intestine Large	intestine
2	chr15:57425800-57442200	Weak transcription	Right Ventricle	heart
3	chr15:57427400-57442600	Weak transcription	Sigmoid Colon	Sigmoid Colon
4	chr15:57428400-57442200	Weak transcription	Primary T cells from cord blood	blood
5	chr15:57428600-57444000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
6	chr15:57433000-57444000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:57436000-57442200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr15:57437200-57442600	Weak transcription	K562	blood
9	chr15:57437800-57442000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:57438400-57442800	Enhancers	Breast Myoepithelial Primary Cells	Breast
11	chr15:57438600-57444000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
12	chr15:57439000-57442800	Enhancers	Brain Substantia Nigra	brain
13	chr15:57439000-57463400	Weak transcription	Rectal Mucosa Donor 31	rectum
14	chr15:57439200-57442200	Weak transcription	Primary hematopoietic stem cells	blood
15	chr15:57439200-57442400	Enhancers	Brain Cingulate Gyrus	brain
16	chr15:57439200-57442400	Enhancers	Colon Smooth Muscle	Colon
17	chr15:57439200-57442600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr15:57439200-57442800	Enhancers	Cortex derived primary cultured neurospheres	brain
19	chr15:57439200-57442800	Enhancers	Brain Angular Gyrus	brain
20	chr15:57439200-57443400	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:57439200-57443600	Weak transcription	H1 Cell Line	embryonic stem cell
22	chr15:57439200-57443600	Weak transcription	A549	lung
23	chr15:57439200-57443800	Weak transcription	Primary T helper cells PMA-I stimulated	--
24	chr15:57439400-57442200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr15:57439400-57442200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr15:57439400-57442200	Weak transcription	HSMM	muscle
27	chr15:57439400-57442400	Enhancers	Rectal Smooth Muscle	rectum
28	chr15:57439400-57442600	Enhancers	Brain Anterior Caudate	brain
29	chr15:57439400-57442600	Enhancers	Brain Hippocampus Middle	brain
30	chr15:57439400-57443000	Enhancers	Adipose Nuclei	Adipose
31	chr15:57439400-57443200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
32	chr15:57439400-57443200	Weak transcription	Fetal Intestine Small	intestine
33	chr15:57439400-57443600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr15:57439400-57444000	Weak transcription	HUES48 Cell Line	embryonic stem cell
35	chr15:57439400-57444000	Weak transcription	Rectal Mucosa Donor 29	rectum
36	chr15:57439400-57456000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
37	chr15:57439400-57491600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
38	chr15:57439600-57444000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
39	chr15:57440000-57442200	Weak transcription	Fetal Kidney	kidney
40	chr15:57440000-57442600	Enhancers	Skeletal Muscle Male	skeletal muscle
41	chr15:57440400-57442400	Weak transcription	Primary B cells from cord blood	blood
42	chr15:57440400-57442800	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
43	chr15:57440400-57443200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
44	chr15:57440400-57443200	Strong transcription	Fetal Thymus	thymus
45	chr15:57440400-57444000	Weak transcription	Duodenum Mucosa	Duodenum
46	chr15:57440600-57442800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
47	chr15:57440600-57442800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
48	chr15:57440600-57442800	Enhancers	HSMMtube	muscle
49	chr15:57440600-57442800	Enhancers	Osteobl	bone
50	chr15:57440600-57443400	Weak transcription	Primary B cells from peripheral blood	blood

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