Variant report

Variant	rs2264904
Chromosome Location	chr15:57373739-57373740
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:57373645..57376211-chr15:57382766..57385379,2	K562	blood:

Extended variants
information (count: 59 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:56)

rs_ID	r²[population]
rs11071305	0.82[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11635645	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12900589	0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900874	0.85[EUR][1000 genomes]
rs12910170	0.80[ASN][1000 genomes]
rs13313455	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1820995	0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2169465	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs2435907	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439918	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439919	0.87[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2464429	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2464430	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2464431	0.83[AMR][1000 genomes]
rs2470079	0.83[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2470082	0.86[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2585088	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585112	0.89[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2615231	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2703576	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703577	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2703580	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2733170	0.80[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2733177	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733182	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733185	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2733188	0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2733307	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733332	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28414972	0.88[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28514688	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs28648502	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28712697	0.82[AFR][1000 genomes]
rs2920264	0.84[EUR][1000 genomes]
rs2920265	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2920267	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920269	0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2927189	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2951895	0.86[AMR][1000 genomes];0.85[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951898	0.92[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951899	0.94[AFR][1000 genomes];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951901	0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2951903	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2951904	0.85[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2951906	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2957574	0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2957591	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2962990	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2962991	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2962992	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs6493901	0.80[ASN][1000 genomes]
rs7163267	0.86[AFR][1000 genomes]
rs7168387	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7173936	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs8037901	0.88[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs967514	0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.87[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
rs2264904	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:77 , 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	chr15:57346000-57374400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr15:57350400-57374000	Weak transcription	Ovary	ovary
4	chr15:57353800-57373800	Weak transcription	Left Ventricle	heart
5	chr15:57353800-57406400	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:57354200-57384600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
7	chr15:57355000-57374000	Weak transcription	Osteobl	bone
8	chr15:57356000-57393400	Weak transcription	Thymus	Thymus
9	chr15:57356400-57373800	Weak transcription	Fetal Muscle Trunk	muscle
10	chr15:57362800-57384200	Weak transcription	HepG2	liver
11	chr15:57363800-57378200	Weak transcription	Gastric	stomach
12	chr15:57363800-57382000	Weak transcription	Right Atrium	heart
13	chr15:57365200-57374200	Weak transcription	Fetal Kidney	kidney
14	chr15:57365200-57384000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr15:57365400-57374000	Weak transcription	NHEK	skin
16	chr15:57365600-57385200	Weak transcription	HSMM	muscle
17	chr15:57365800-57374200	Weak transcription	A549	lung
18	chr15:57365800-57384000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
19	chr15:57367000-57374000	Weak transcription	Psoas Muscle	Psoas
20	chr15:57368000-57380400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr15:57371600-57375000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
22	chr15:57371600-57375200	Enhancers	HUVEC	blood vessel
23	chr15:57371800-57374800	Enhancers	Duodenum Smooth Muscle	Duodenum
24	chr15:57371800-57375000	Enhancers	K562	blood
25	chr15:57371800-57382400	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr15:57372000-57384000	Weak transcription	Dnd41	blood
27	chr15:57372400-57375200	Enhancers	Fetal Heart	heart
28	chr15:57372600-57373800	Enhancers	Brain Hippocampus Middle	brain
29	chr15:57372600-57374000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
30	chr15:57372600-57374000	Enhancers	Small Intestine	intestine
31	chr15:57372600-57374200	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:57372600-57375000	Enhancers	Duodenum Mucosa	Duodenum
33	chr15:57372600-57375000	Enhancers	Pancreatic Islets	Pancreatic Islet
34	chr15:57372600-57386000	Weak transcription	iPS-18 Cell Line	embryonic stem cell
35	chr15:57372600-57404000	Weak transcription	HSMMtube	muscle
36	chr15:57372600-57404200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr15:57372800-57374000	Weak transcription	Primary T helper cells PMA-I stimulated	--
38	chr15:57372800-57374200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
39	chr15:57372800-57374200	Weak transcription	Colon Smooth Muscle	Colon
40	chr15:57372800-57374200	Weak transcription	Stomach Mucosa	stomach
41	chr15:57372800-57374200	Weak transcription	NH-A	brain
42	chr15:57372800-57374400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr15:57372800-57374400	Genic enhancers	Fetal Thymus	thymus
44	chr15:57372800-57374800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr15:57372800-57375000	Enhancers	Primary hematopoietic stem cells	blood
46	chr15:57372800-57375000	Enhancers	Brain Cingulate Gyrus	brain
47	chr15:57372800-57375000	Enhancers	Fetal Lung	lung
48	chr15:57372800-57379000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
49	chr15:57372800-57380800	Weak transcription	Right Ventricle	heart
50	chr15:57372800-57384000	Weak transcription	HUES64 Cell Line	embryonic stem cell

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