Variant report

Variant	rs2464431
Chromosome Location	chr15:57366096-57366097
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57364693..57367235-chr15:57380279..57382303,2	K562	blood:

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs11856411	0.81[AFR][1000 genomes]
rs12900874	0.81[AMR][1000 genomes]
rs1820995	0.85[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2264904	0.83[AMR][1000 genomes]
rs2435907	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2439918	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2439919	0.91[AMR][1000 genomes];0.84[ASN][1000 genomes]
rs2464429	0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2464430	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470079	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2470082	0.84[AFR][1000 genomes];0.92[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2585088	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2585102	0.81[ASN][1000 genomes]
rs2585112	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703576	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2703577	0.85[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703580	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2733170	0.86[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs2733174	0.81[ASN][1000 genomes]
rs2733177	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733182	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733185	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733188	0.87[AMR][1000 genomes]
rs28422021	0.81[AFR][1000 genomes]
rs28541606	0.81[AFR][1000 genomes]
rs2920264	0.85[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2920265	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2920267	0.86[AFR][1000 genomes];0.89[AMR][1000 genomes];0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2920269	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2951895	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.87[ASN][1000 genomes]
rs2951901	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2951903	0.92[AFR][1000 genomes];0.95[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2951904	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.83[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2951906	0.82[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957574	0.91[AMR][1000 genomes];0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2957591	0.80[AMR][1000 genomes]
rs2962990	0.87[AMR][1000 genomes];0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2962991	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2962992	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2962993	0.81[ASN][1000 genomes]
rs4559854	0.82[AMR][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
rs2464431	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:63 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
2	chr15:57336600-57371800	Weak transcription	K562	blood
3	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
4	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
6	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
7	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
8	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
9	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
10	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
11	chr15:57350400-57374000	Weak transcription	Ovary	ovary
12	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
13	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
14	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
15	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr15:57354600-57371600	Weak transcription	NH-A	brain
18	chr15:57355000-57374000	Weak transcription	Osteobl	bone
19	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
20	chr15:57356400-57370800	Weak transcription	Primary hematopoietic stem cells	blood
21	chr15:57356400-57371000	Weak transcription	Dnd41	blood
22	chr15:57356400-57371800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
23	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
24	chr15:57356600-57372000	Weak transcription	Primary B cells from cord blood	blood
25	chr15:57356800-57371200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
26	chr15:57357600-57366600	Weak transcription	Primary B cells from peripheral blood	blood
27	chr15:57357600-57371600	Weak transcription	HUVEC	blood vessel
28	chr15:57360200-57371800	Weak transcription	Duodenum Smooth Muscle	Duodenum
29	chr15:57360400-57372400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
30	chr15:57360600-57371600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
31	chr15:57362000-57366200	Weak transcription	Primary neutrophils fromperipheralblood	blood
32	chr15:57362400-57371200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr15:57362800-57371000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
34	chr15:57362800-57384200	Weak transcription	HepG2	liver
35	chr15:57363000-57372600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr15:57363200-57371600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
37	chr15:57363800-57378200	Weak transcription	Gastric	stomach
38	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
39	chr15:57364800-57371400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
40	chr15:57365000-57371600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
41	chr15:57365200-57370800	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr15:57365200-57370800	Strong transcription	Fetal Thymus	thymus
43	chr15:57365200-57374200	Weak transcription	Fetal Kidney	kidney
44	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
45	chr15:57365400-57366600	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr15:57365400-57366800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:57365400-57370600	Weak transcription	Primary T cells from cord blood	blood
48	chr15:57365400-57371400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr15:57365400-57371400	Weak transcription	GM12878-XiMat	blood
50	chr15:57365400-57371600	Weak transcription	ES-I3 Cell Line	embryonic stem cell

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