Variant report

Variant	rs1346165
Chromosome Location	chr15:73077953-73077954
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POU2F2	chr15:73077646-73078142	GM12878	blood:	n/a	n/a
2	RAD21	chr15:73077617-73078252	IMR90	lung:	n/a	n/a
3	POLR2A	chr15:73077807-73078159	GM12878	blood:	n/a	n/a
4	PAX5	chr15:73077623-73078174	GM12878	blood:	n/a	n/a
5	TCF12	chr15:73077834-73078128	GM12878	blood:	n/a	n/a
6	TBL1XR1	chr15:73077849-73077989	GM12878	blood:	n/a	n/a
7	SMC3	chr15:73077840-73077993	GM12878	blood:	n/a	n/a
8	SP1	chr15:73077630-73078193	GM12878	blood:	n/a	n/a
9	CTCF	chr15:73077880-73078030	HAc	cerebellar:	n/a	chr15:73077898-73077906
10	EBF1	chr15:73077585-73078194	GM12878	blood:	n/a	n/a
11	PAX5	chr15:73077823-73078049	GM12878	blood:	n/a	n/a
12	EBF1	chr15:73077787-73078091	GM12878	blood:	n/a	n/a
13	POLR2A	chr15:73077828-73078247	IMR90	lung:	n/a	n/a
14	CHD1	chr15:73077857-73078031	GM12878	blood:	n/a	n/a
15	RUNX3	chr15:73077682-73078143	GM12878	blood:	n/a	chr15:73077853-73077868
16	CTCF	chr15:73077840-73077990	GM06990	blood:	n/a	chr15:73077877-73077890 chr15:73077898-73077906
17	BHLHE40	chr15:73077801-73078122	GM12878	blood:	n/a	n/a
18	POLR2A	chr15:73077933-73078123	GM12878	blood:	n/a	n/a
19	ESRRA	chr15:73074606-73078362	GM12878	blood:	n/a	n/a
20	EBF1	chr15:73077223-73078234	GM12878	blood:	n/a	n/a
21	CHD2	chr15:73077749-73078116	GM12878	blood:	n/a	n/a
22	PAX5	chr15:73077804-73077955	GM12878	blood:	n/a	n/a
23	RUNX3	chr15:73077518-73078233	GM12878	blood:	n/a	chr15:73077853-73077868
24	EP300	chr15:73077753-73078039	GM12878	blood:	n/a	n/a
25	MAZ	chr15:73074762-73078225	IMR90	lung:	n/a	chr15:73077887-73077896
26	RFX5	chr15:73077849-73078049	HepG2	liver:	n/a	chr15:73077887-73077896 chr15:73077886-73077901 chr15:73077883-73077898 chr15:73077884-73077898 chr15:73077886-73077901 chr15:73077885-73077902
27	MXI1	chr15:73077739-73078060	GM12878	blood:	n/a	chr15:73077887-73077902
28	EP300	chr15:73077432-73078143	GM12878	blood:	n/a	n/a
29	EP300	chr15:73077830-73077981	GM12878	blood:	n/a	n/a
30	RCOR1	chr15:73077939-73077961	HepG2	liver:	n/a	n/a
31	SP1	chr15:73077654-73078181	GM12878	blood:	n/a	n/a
32	CTCF	chr15:73077840-73077990	HCPEpiC	choroid plexus:	n/a	chr15:73077877-73077890 chr15:73077898-73077906
33	CTCF	chr15:73077860-73078010	HBMEC	blood vessel:	n/a	chr15:73077877-73077890 chr15:73077898-73077906
34	MAZ	chr15:73077715-73078046	GM12878	blood:	n/a	chr15:73077887-73077896
35	POLR2A	chr15:73077856-73078227	U87	brain:	n/a	n/a
36	RFX5	chr15:73077873-73077991	GM12878	blood:	n/a	chr15:73077887-73077896 chr15:73077886-73077901 chr15:73077883-73077898 chr15:73077884-73077898 chr15:73077886-73077901 chr15:73077885-73077902

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:73075212..73078087-chr15:73342810..73345457,4	MCF-7	breast:
2	chr15:73074691..73078350-chr15:73341676..73346479,5	MCF-7	breast:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-BBS4-1	chr15:73077862-73078031	NONHSAT047127

Variant related genes	Relation type
ADPGK	TF binding region
ENSG00000067141	Chromatin interaction

Extended variants
information (count: 45 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11072380	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs11072383	0.84[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap]
rs11072389	0.86[ASN][1000 genomes]
rs12437473	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs12439200	0.92[CHB][hapmap];0.96[CHD][hapmap];0.86[ASN][1000 genomes]
rs12439473	0.86[ASN][1000 genomes]
rs12591690	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12591728	1.00[CEU][hapmap];0.84[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12594320	0.96[CHD][hapmap];0.89[GIH][hapmap];0.81[ASN][1000 genomes]
rs12898814	0.86[ASW][hapmap];1.00[CEU][hapmap];0.84[CHB][hapmap];0.89[CHD][hapmap];0.94[GIH][hapmap];0.94[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs12902361	0.86[EUR][1000 genomes]
rs12906007	0.84[CHB][hapmap]
rs12916236	0.85[ASN][1000 genomes]
rs12916448	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs16957257	0.86[EUR][1000 genomes]
rs16957297	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.88[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2162268	0.91[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2304598	0.92[CHB][hapmap];0.85[ASN][1000 genomes]
rs28397892	0.94[AFR][1000 genomes];0.95[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs28562097	0.83[ASN][1000 genomes]
rs28648660	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28737436	0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28801790	0.85[ASN][1000 genomes]
rs28827493	0.86[ASN][1000 genomes]
rs28866048	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs33923961	0.91[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs34660767	0.85[ASN][1000 genomes]
rs34940604	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs4777541	0.92[CHB][hapmap];0.86[ASN][1000 genomes]
rs6495017	0.98[ASN][1000 genomes]
rs6495018	0.89[CHD][hapmap]
rs7162166	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7170394	0.84[CHB][hapmap]
rs7172397	0.84[CHB][hapmap]
rs7182854	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8023358	0.92[CHB][hapmap];0.96[CHD][hapmap];0.89[GIH][hapmap];0.80[ASN][1000 genomes]
rs8024644	0.80[ASN][1000 genomes]
rs8026286	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes]
rs8026559	0.84[CHB][hapmap];0.96[CHD][hapmap]
rs8031691	1.00[CEU][hapmap];0.92[CHB][hapmap];0.96[CHD][hapmap];1.00[GIH][hapmap];0.86[MEX][hapmap];1.00[TSI][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8036269	0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv2758386	chr15:72819785-73120560	Strong transcription ZNF genes & repeats Weak transcription Enhancers Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	esv2760039	chr15:72819785-73120560	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
3	nsv428307	chr15:72819785-73120560	Strong transcription Flanking Active TSS Active TSS Weak transcription ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
4	nsv482512	chr15:73023099-73175952	Flanking Active TSS Strong transcription Weak transcription Enhancers ZNF genes & repeats Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	25 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:65 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:73076800-73078600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr15:73077000-73078000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
3	chr15:73077000-73078000	Enhancers	Fetal Stomach	stomach
4	chr15:73077000-73078200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr15:73077000-73078200	Enhancers	Fetal Muscle Leg	muscle
6	chr15:73077000-73078400	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr15:73077000-73078400	Enhancers	Fetal Muscle Trunk	muscle
8	chr15:73077000-73078600	Enhancers	Primary hematopoietic stem cells	blood
9	chr15:73077000-73078600	Enhancers	NH-A	brain
10	chr15:73077000-73078800	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
11	chr15:73077000-73079000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
13	chr15:73077000-73079600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr15:73077000-73080600	Enhancers	HSMMtube	muscle
15	chr15:73077000-73088800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:73077200-73078000	Enhancers	Brain Inferior Temporal Lobe	brain
17	chr15:73077200-73078200	Enhancers	Primary T killer memory cells from peripheral blood	blood
18	chr15:73077200-73078200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr15:73077200-73078200	Enhancers	Brain Anterior Caudate	brain
20	chr15:73077200-73078200	Enhancers	Fetal Brain Female	brain
21	chr15:73077200-73078200	Enhancers	Fetal Thymus	thymus
22	chr15:73077200-73078200	Enhancers	Skeletal Muscle Female	skeletal muscle
23	chr15:73077200-73078200	Enhancers	HSMM	muscle
24	chr15:73077200-73078400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
25	chr15:73077200-73078400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
26	chr15:73077200-73078400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
27	chr15:73077200-73078600	Enhancers	NHDF-Ad	bronchial
28	chr15:73077200-73078600	Enhancers	Osteobl	bone
29	chr15:73077200-73078800	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr15:73077200-73079000	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
31	chr15:73077200-73079200	Enhancers	Primary T helper cells PMA-I stimulated	--
32	chr15:73077200-73079200	Enhancers	Cortex derived primary cultured neurospheres	brain
33	chr15:73077200-73079400	Enhancers	Primary T cells fromperipheralblood	blood
34	chr15:73077200-73079400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
35	chr15:73077200-73079400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
36	chr15:73077200-73079600	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
37	chr15:73077200-73079800	Enhancers	Breast Myoepithelial Primary Cells	Breast
38	chr15:73077200-73079800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
39	chr15:73077200-73079800	Enhancers	Brain Substantia Nigra	brain
40	chr15:73077200-73080000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
41	chr15:73077200-73080000	Enhancers	Primary T helper cells fromperipheralblood	blood
42	chr15:73077200-73080000	Enhancers	GM12878-XiMat	blood
43	chr15:73077200-73080200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
44	chr15:73077200-73080400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
45	chr15:73077200-73080600	Enhancers	Brain Hippocampus Middle	brain
46	chr15:73077200-73081200	Enhancers	Fetal Brain Male	brain
47	chr15:73077400-73078000	Weak transcription	Gastric	stomach
48	chr15:73077400-73078000	Enhancers	Dnd41	blood
49	chr15:73077400-73078200	Enhancers	Duodenum Mucosa	Duodenum
50	chr15:73077400-73078400	Enhancers	Skeletal Muscle Male	skeletal muscle

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