Variant report

Variant	rs12898844
Chromosome Location	chr15:57358508-57358509
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57352117..57354569-chr15:57356374..57360031,3	K562	blood:
2	chr15:57352117..57354489-chr15:57357081..57359694,2	K562	blood:

Extended variants
information (count: 86 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:83)

rs_ID	r²[population]
rs11071305	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11630195	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11631228	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs11631541	0.90[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11853331	0.82[EUR][1000 genomes]
rs11858471	0.85[EUR][1000 genomes]
rs12898327	0.82[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12899187	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12899915	0.86[AMR][1000 genomes];0.90[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12900589	0.82[ASN][1000 genomes]
rs12900874	0.87[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12900986	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12901780	0.82[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12904070	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905900	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12906873	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12906936	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12909811	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs12910094	0.82[EUR][1000 genomes]
rs12912007	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914182	0.85[EUR][1000 genomes]
rs12914410	0.83[EUR][1000 genomes]
rs12914625	0.85[EUR][1000 genomes]
rs12916237	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12916958	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs12917247	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1430823	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1628067	0.83[EUR][1000 genomes]
rs17239040	0.86[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs17819700	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs1820995	0.86[ASN][1000 genomes]
rs2111891	0.82[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs2116065	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2116066	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2414490	0.86[EUR][1000 genomes]
rs2414494	0.81[EUR][1000 genomes]
rs2435907	0.86[ASN][1000 genomes]
rs2439918	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2439919	0.81[ASN][1000 genomes]
rs2464429	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2464430	0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2470079	0.84[ASN][1000 genomes]
rs2470082	0.85[ASN][1000 genomes]
rs2583108	0.87[EUR][1000 genomes]
rs2585082	0.86[EUR][1000 genomes]
rs2585087	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2585088	0.85[ASN][1000 genomes]
rs2585102	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2585112	0.83[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2703576	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2703577	0.83[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703580	0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733170	0.83[ASN][1000 genomes]
rs2733171	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2733174	0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733176	0.89[EUR][1000 genomes]
rs2733177	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2733182	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2733185	0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2920264	0.82[ASN][1000 genomes]
rs2920265	0.85[ASN][1000 genomes]
rs2920267	0.81[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2920269	0.84[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2951895	0.88[ASN][1000 genomes]
rs2951901	0.85[ASN][1000 genomes]
rs2951903	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2951904	0.81[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2951906	0.85[ASN][1000 genomes]
rs2957574	0.85[ASN][1000 genomes]
rs2962990	0.80[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2962991	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2962992	0.81[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2962993	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs34262415	0.84[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs35646942	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs3803454	0.82[EUR][1000 genomes]
rs4774902	0.83[EUR][1000 genomes]
rs4774910	0.90[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs62022986	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs62022988	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs6493901	0.91[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs7170133	0.97[AMR][1000 genomes];0.86[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7496293	0.84[EUR][1000 genomes];0.83[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
rs12898844	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:78 , 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	chr15:57339800-57361600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr15:57340200-57372600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
5	chr15:57343800-57363400	Weak transcription	Aorta	Aorta
6	chr15:57344600-57363600	Weak transcription	Right Atrium	heart
7	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
8	chr15:57347000-57373400	Weak transcription	Fetal Intestine Small	intestine
9	chr15:57347600-57373000	Weak transcription	Rectal Mucosa Donor 31	rectum
10	chr15:57347600-57373200	Weak transcription	Fetal Intestine Large	intestine
11	chr15:57348200-57361800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr15:57349600-57359800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
13	chr15:57349800-57363800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:57349800-57366600	Weak transcription	Psoas Muscle	Psoas
15	chr15:57350200-57360800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
16	chr15:57350200-57363800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr15:57350400-57362400	Weak transcription	Primary T helper cells fromperipheralblood	blood
18	chr15:57350400-57372400	Weak transcription	Fetal Lung	lung
19	chr15:57350400-57373400	Weak transcription	Primary T cells fromperipheralblood	blood
20	chr15:57350400-57374000	Weak transcription	Ovary	ovary
21	chr15:57351600-57361600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:57351800-57359000	Weak transcription	GM12878-XiMat	blood
23	chr15:57351800-57360000	Weak transcription	Sigmoid Colon	Sigmoid Colon
24	chr15:57351800-57361600	Weak transcription	Primary T cells from cord blood	blood
25	chr15:57351800-57371000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
26	chr15:57353000-57361600	Strong transcription	Fetal Thymus	thymus
27	chr15:57353200-57359800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
28	chr15:57353200-57362800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:57353400-57362600	Weak transcription	HUES48 Cell Line	embryonic stem cell
30	chr15:57353400-57371000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:57353600-57362400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
32	chr15:57353600-57364200	Weak transcription	HUES6 Cell Line	embryonic stem cell
33	chr15:57353800-57362000	Weak transcription	HepG2	liver
34	chr15:57353800-57363800	Weak transcription	Colon Smooth Muscle	Colon
35	chr15:57353800-57364800	Weak transcription	HSMM	muscle
36	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
37	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
38	chr15:57354200-57361800	Weak transcription	NHDF-Ad	bronchial
39	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr15:57354600-57359200	Weak transcription	Monocytes-CD14+_RO01746	blood
41	chr15:57354600-57371600	Weak transcription	NH-A	brain
42	chr15:57355000-57374000	Weak transcription	Osteobl	bone
43	chr15:57355200-57359000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
44	chr15:57355200-57359800	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr15:57355400-57365000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr15:57356000-57359800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
47	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
48	chr15:57356200-57360000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:57356400-57359200	Weak transcription	HMEC	breast
50	chr15:57356400-57359800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin

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