Variant report

Variant	rs2435907
Chromosome Location	chr15:57333416-57333417
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	chr15:57331807..57334195-chr15:57336717..57338701,2	K562	blood:

Extended variants
information (count: 71 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:66)

rs_ID	r²[population]
rs11631541	0.81[ASN][1000 genomes]
rs11635645	0.82[EUR][1000 genomes]
rs12898327	0.80[ASN][1000 genomes]
rs12898844	0.86[ASN][1000 genomes]
rs12900589	0.84[EUR][1000 genomes]
rs12900874	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12905900	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs12917247	0.81[ASN][1000 genomes]
rs13313455	0.83[EUR][1000 genomes]
rs1430823	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs16977222	0.81[AFR][1000 genomes]
rs1820995	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2264904	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2439918	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2439919	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2464429	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2464430	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2464431	0.81[AFR][1000 genomes];0.89[AMR][1000 genomes];0.81[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2470079	0.93[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2470082	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585087	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2585088	0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2585102	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2585112	0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2615231	0.83[EUR][1000 genomes]
rs2703576	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2703577	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2703580	0.85[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2733170	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2733171	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733174	0.85[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733176	0.85[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2733177	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733182	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2733185	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2733188	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2733307	0.82[EUR][1000 genomes]
rs2733332	0.87[EUR][1000 genomes]
rs28414972	0.83[EUR][1000 genomes]
rs28514688	0.83[EUR][1000 genomes]
rs28533433	0.80[AFR][1000 genomes]
rs28648502	0.83[EUR][1000 genomes]
rs2920264	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2920265	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2920267	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2920269	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2927189	0.87[EUR][1000 genomes]
rs2951895	0.91[AFR][1000 genomes];0.98[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2951898	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2951899	0.80[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2951901	0.85[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2951903	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951904	0.88[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2951906	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957574	0.96[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2957591	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs2962990	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2962991	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2962992	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2962993	0.83[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4559854	0.87[AMR][1000 genomes]
rs62022988	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7168387	0.84[EUR][1000 genomes]
rs7171073	0.81[AFR][1000 genomes]
rs7171304	0.80[AFR][1000 genomes]
rs967514	0.83[EUR][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
rs2435907	TCF12	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:57309400-57334600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
2	chr15:57311000-57347000	Weak transcription	Fetal Intestine Large	intestine
3	chr15:57316400-57345400	Weak transcription	Fetal Intestine Small	intestine
4	chr15:57318600-57335600	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
5	chr15:57324200-57337800	Weak transcription	Psoas Muscle	Psoas
6	chr15:57324200-57339000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
7	chr15:57324200-57341200	Weak transcription	Fetal Stomach	stomach
8	chr15:57324400-57338000	Weak transcription	HSMM	muscle
9	chr15:57324400-57341200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
10	chr15:57324400-57349200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
11	chr15:57324600-57355800	Weak transcription	Primary B cells from cord blood	blood
12	chr15:57324600-57398600	Weak transcription	Fetal Muscle Leg	muscle
13	chr15:57324800-57347200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr15:57324800-57349400	Weak transcription	Right Ventricle	heart
15	chr15:57325000-57334600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
16	chr15:57326400-57341000	Weak transcription	Muscle Satellite Cultured Cells	--
17	chr15:57328200-57353600	Weak transcription	Pancreas	Pancrea
18	chr15:57328400-57333600	Weak transcription	H9 Cell Line	embryonic stem cell
19	chr15:57328400-57341200	Weak transcription	Ovary	ovary
20	chr15:57328400-57343800	Weak transcription	Small Intestine	intestine
21	chr15:57328400-57345800	Weak transcription	Left Ventricle	heart
22	chr15:57328600-57355000	Weak transcription	Dnd41	blood
23	chr15:57328800-57336400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr15:57329800-57334000	Enhancers	iPS-18 Cell Line	embryonic stem cell
25	chr15:57329800-57349600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
26	chr15:57329800-57351400	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
27	chr15:57330200-57334600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
28	chr15:57330400-57343400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
29	chr15:57330600-57335400	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
30	chr15:57330600-57335800	Enhancers	Brain Substantia Nigra	brain
31	chr15:57330600-57337000	Weak transcription	Fetal Thymus	thymus
32	chr15:57330800-57334200	Enhancers	iPS-15b Cell Line	embryonic stem cell
33	chr15:57330800-57334600	Enhancers	HUES64 Cell Line	embryonic stem cell
34	chr15:57330800-57337400	Enhancers	HUES48 Cell Line	embryonic stem cell
35	chr15:57331000-57333600	Enhancers	Primary T cells from cord blood	blood
36	chr15:57331600-57334000	Weak transcription	Fetal Kidney	kidney
37	chr15:57331800-57334200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr15:57331800-57335400	Enhancers	Brain Inferior Temporal Lobe	brain
39	chr15:57331800-57338200	Enhancers	Brain Cingulate Gyrus	brain
40	chr15:57331800-57341200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:57332000-57334600	Weak transcription	H1 Cell Line	embryonic stem cell
42	chr15:57332000-57335200	Weak transcription	Fetal Heart	heart
43	chr15:57332000-57337000	Weak transcription	GM12878-XiMat	blood
44	chr15:57332000-57337800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr15:57332000-57345200	Weak transcription	HepG2	liver
46	chr15:57332000-57346000	Weak transcription	Primary hematopoietic stem cells	blood
47	chr15:57332000-57349200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
48	chr15:57332000-57349400	Weak transcription	Thymus	Thymus
49	chr15:57332000-57355800	Weak transcription	Primary B cells from peripheral blood	blood
50	chr15:57332200-57333600	Enhancers	Brain Anterior Caudate	brain

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