Variant report

Variant	rs62022988
Chromosome Location	chr15:57325187-57325188
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	chr15:57209392..57212230-chr15:57324086..57325736,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000140262	Chromatin interaction
ENSG00000137871	Chromatin interaction

Extended variants
information (count: 90 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:85)

rs_ID	r²[population]
rs11071305	0.86[EUR][1000 genomes]
rs11630195	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11631228	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11631541	0.91[AMR][1000 genomes];0.85[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11853331	0.84[AMR][1000 genomes]
rs11858471	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12898327	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12898844	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12899187	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12899915	0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12900874	0.89[ASN][1000 genomes]
rs12900986	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12901780	0.94[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12903578	0.85[AMR][1000 genomes]
rs12904070	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs12905900	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12906873	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12906936	0.99[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12908670	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs12909811	0.96[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12910094	0.87[AMR][1000 genomes]
rs12912007	0.80[EUR][1000 genomes]
rs12914182	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs12914410	0.85[AMR][1000 genomes];0.80[EUR][1000 genomes]
rs12914625	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12915473	0.84[AMR][1000 genomes]
rs12916237	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12916958	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12917247	0.94[AMR][1000 genomes];0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1430823	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1628067	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs17239040	0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs17819700	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1820995	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2053472	0.90[AMR][1000 genomes]
rs2111891	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2116065	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2116066	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs213164	0.90[AMR][1000 genomes]
rs2414490	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2414494	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2435907	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2439918	0.82[ASN][1000 genomes]
rs2464429	0.83[ASN][1000 genomes]
rs2464430	0.81[ASN][1000 genomes]
rs2470079	0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470082	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2583108	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2585082	0.90[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2585087	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2585088	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2585102	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2585112	0.81[ASN][1000 genomes]
rs2703576	0.81[ASN][1000 genomes]
rs2703577	0.82[ASN][1000 genomes]
rs2703580	0.82[ASN][1000 genomes]
rs2733170	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2733171	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2733174	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2733176	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2733177	0.82[ASN][1000 genomes]
rs2733181	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs2920264	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920265	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2920267	0.82[ASN][1000 genomes]
rs2920269	0.81[ASN][1000 genomes]
rs2951895	0.81[ASN][1000 genomes]
rs2951901	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2951906	0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2957574	0.83[ASN][1000 genomes]
rs2962990	0.82[ASN][1000 genomes]
rs2962991	0.83[ASN][1000 genomes]
rs2962992	0.82[ASN][1000 genomes]
rs2962993	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs34262415	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs35646942	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs3803454	0.92[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774899	0.90[AMR][1000 genomes]
rs4774902	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs4774910	0.81[EUR][1000 genomes]
rs62022986	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs62025331	0.92[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs6493901	0.81[EUR][1000 genomes]
rs7170133	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs7496293	0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	nsv542393	chr15:57115116-57341363	Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases
3	nsv1052052	chr15:57232111-57344561	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
4	nsv542394	chr15:57232111-57344561	Enhancers Weak transcription Genic enhancers ZNF genes & repeats Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62022988	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57308000-57328000	Weak transcription	Gastric	stomach
2	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
3	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
4	chr15:57315600-57328200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
5	chr15:57315600-57328600	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr15:57316400-57328200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
7	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
8	chr15:57316600-57327800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr15:57317600-57326200	Weak transcription	Esophagus	oesophagus
10	chr15:57318600-57331000	Weak transcription	Fetal Kidney	kidney
11	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:57320600-57325200	Enhancers	Brain Substantia Nigra	brain
13	chr15:57322400-57326600	Enhancers	Brain Angular Gyrus	brain
14	chr15:57322800-57326200	Enhancers	HUES64 Cell Line	embryonic stem cell
15	chr15:57323000-57325200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr15:57323600-57325600	Weak transcription	Stomach Mucosa	stomach
17	chr15:57323600-57325600	Weak transcription	HepG2	liver
18	chr15:57323600-57328000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
19	chr15:57323800-57327600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:57323800-57329400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
21	chr15:57324200-57325600	Weak transcription	Liver	Liver
22	chr15:57324200-57327600	Weak transcription	Pancreas	Pancrea
23	chr15:57324200-57327800	Weak transcription	Duodenum Mucosa	Duodenum
24	chr15:57324200-57328000	Weak transcription	Primary T cells from cord blood	blood
25	chr15:57324200-57328200	Weak transcription	Primary T helper cells fromperipheralblood	blood
26	chr15:57324200-57328200	Weak transcription	HSMMtube	muscle
27	chr15:57324200-57328400	Weak transcription	Primary hematopoietic stem cells	blood
28	chr15:57324200-57328600	Weak transcription	GM12878-XiMat	blood
29	chr15:57324200-57329400	Weak transcription	Primary B cells from peripheral blood	blood
30	chr15:57324200-57331400	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr15:57324200-57331800	Weak transcription	Skeletal Muscle Female	skeletal muscle
32	chr15:57324200-57332600	Weak transcription	Fetal Lung	lung
33	chr15:57324200-57337800	Weak transcription	Psoas Muscle	Psoas
34	chr15:57324200-57339000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
35	chr15:57324200-57341200	Weak transcription	Fetal Stomach	stomach
36	chr15:57324400-57325200	Enhancers	Brain Hippocampus Middle	brain
37	chr15:57324400-57325600	Weak transcription	HUES48 Cell Line	embryonic stem cell
38	chr15:57324400-57325600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
39	chr15:57324400-57325600	Weak transcription	A549	lung
40	chr15:57324400-57326000	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr15:57324400-57326000	Weak transcription	Osteobl	bone
42	chr15:57324400-57326200	Enhancers	Brain Anterior Caudate	brain
43	chr15:57324400-57327400	Weak transcription	Fetal Thymus	thymus
44	chr15:57324400-57327400	Weak transcription	K562	blood
45	chr15:57324400-57327600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr15:57324400-57327600	Weak transcription	Thymus	Thymus
47	chr15:57324400-57327800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr15:57324400-57327800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
49	chr15:57324400-57327800	Weak transcription	HUES6 Cell Line	embryonic stem cell
50	chr15:57324400-57327800	Weak transcription	iPS-18 Cell Line	embryonic stem cell

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