Variant report

Variant	rs60397096
Chromosome Location	chr15:52396085-52396086
allele	A/C
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	POLR2A	chr15:52395680-52396301	GM12878	blood:	n/a	n/a
2	FOXM1	chr15:52395554-52396220	GM12878	blood:	n/a	n/a
3	RXRA	chr15:52395471-52396145	SK-N-SH	brain:	n/a	n/a
4	CHD1	chr15:52395428-52396247	GM12878	blood:	n/a	n/a
5	POLR2A	chr15:52395596-52397248	GM12878	blood:	n/a	n/a
6	NFIC	chr15:52395560-52396287	GM12878	blood:	n/a	n/a
7	PAX5	chr15:52395729-52396248	GM12878	blood:	n/a	n/a
8	NFIC	chr15:52395433-52396191	GM12878	blood:	n/a	n/a
9	BATF	chr15:52395675-52396236	GM12878	blood:	n/a	chr15:52395843-52395853
10	PBX3	chr15:52395506-52396127	SK-N-SH	brain:	n/a	n/a
11	MAX	chr15:52395592-52396113	SK-N-SH	brain:	n/a	chr15:52395841-52395850
12	JUND	chr15:52395639-52396086	A549	lung:	n/a	chr15:52395840-52395851 chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
13	FOSL1	chr15:52395540-52396151	HCT-116	colon:	n/a	chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
14	TCF12	chr15:52395267-52396250	SK-N-SH	brain:	n/a	n/a
15	JUND	chr15:52395358-52396249	SK-N-SH	brain:	n/a	chr15:52395840-52395851 chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
16	ZNF384	chr15:52395627-52396281	GM12878	blood:	n/a	n/a
17	CEBPB	chr15:52395438-52396170	GM12878	blood:	n/a	n/a
18	EBF1	chr15:52395477-52396236	GM12878	blood:	n/a	chr15:52395954-52395965
19	PML	chr15:52395506-52396268	GM12878	blood:	n/a	chr15:52395843-52395852
20	POLR2A	chr15:52395735-52396318	GM12878	blood:	n/a	n/a
21	MXI1	chr15:52395442-52396104	GM12878	blood:	n/a	n/a
22	YY1	chr15:52395784-52396102	GM12892	blood:	n/a	n/a
23	EP300	chr15:52395291-52396222	SK-N-SH	brain:	n/a	chr15:52395841-52395850
24	EBF1	chr15:52395647-52396236	GM12878	blood:	n/a	chr15:52395954-52395965
25	SP1	chr15:52395685-52396182	GM12878	blood:	n/a	n/a
26	IRF4	chr15:52395707-52396152	GM12878	blood:	n/a	n/a
27	BCLAF1	chr15:52395632-52396226	GM12878	blood:	n/a	n/a
28	TCF12	chr15:52395356-52396176	SK-N-SH	brain:	n/a	n/a
29	POLR2A	chr15:52395490-52397230	GM12878	blood:	n/a	n/a
30	NFIC	chr15:52395326-52396201	SK-N-SH	brain:	n/a	n/a
31	MTA3	chr15:52395288-52396107	GM12878	blood:	n/a	n/a
32	TCF12	chr15:52395730-52396144	GM12878	blood:	n/a	n/a
33	MAX	chr15:52395705-52396181	GM12878	blood:	n/a	chr15:52395841-52395850
34	PAX5	chr15:52395701-52396109	GM12878	blood:	n/a	n/a
35	POLR2A	chr15:52395720-52396199	GM12891	blood:	n/a	n/a
36	POLR2A	chr15:52395399-52397274	GM12878	blood:	n/a	n/a
37	POLR2A	chr15:52395594-52396414	GM12892	blood:	n/a	n/a
38	ATF2	chr15:52395516-52396205	GM12878	blood:	n/a	n/a
39	CHD2	chr15:52395471-52396136	GM12878	blood:	n/a	n/a
40	JUND	chr15:52395484-52396158	HCT-116	colon:	n/a	chr15:52395840-52395851 chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
41	JUND	chr15:52395349-52396152	SK-N-SH	brain:	n/a	chr15:52395840-52395851 chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
42	POLR2A	chr15:52395666-52396205	GM12891	blood:	n/a	n/a
43	POU2F2	chr15:52395587-52396126	GM12891	blood:	n/a	chr15:52395807-52395816 chr15:52395802-52395820 chr15:52395807-52395817 chr15:52395808-52395815 chr15:52395717-52395732 chr15:52395804-52395819 chr15:52395719-52395734 chr15:52395806-52395818
44	POLR2A	chr15:52395737-52396201	GM12891	blood:	n/a	n/a
45	EP300	chr15:52395569-52396132	GM12878	blood:	n/a	chr15:52395841-52395850
46	JUND	chr15:52395433-52396163	SK-N-SH	brain:	n/a	chr15:52395840-52395851 chr15:52395843-52395850 chr15:52395842-52395850 chr15:52395842-52395850 chr15:52395725-52395737
47	RCOR1	chr15:52395599-52396134	GM12878	blood:	n/a	n/a
48	STAT3	chr15:52395480-52396107	GM12878	blood:	n/a	n/a
49	POLR2A	chr15:52395752-52396230	GM12878	blood:	n/a	n/a
50	RFX5	chr15:52395272-52396357	IMR90	lung:	n/a	chr15:52395791-52395806

No.	Distal block	Cell Line	Cell type
1	chr15:52385306..52387666-chr15:52394870..52397367,3	MCF-7	breast:
2	chr15:52395553..52398772-chr15:52399645..52403144,6	MCF-7	breast:
3	chr15:52394818..52397658-chr15:52475516..52477095,2	MCF-7	breast:
4	chr15:52389305..52392233-chr15:52393391..52397295,3	K562	blood:

Variant related genes	Relation type
ENSG00000259712	TF binding region
ENSG00000242327	Chromatin interaction

Extended variants
information (count: 48 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:43)

rs_ID	r²[population]
rs10400852	1.00[EUR][1000 genomes]
rs16953085	1.00[EUR][1000 genomes]
rs16964735	1.00[EUR][1000 genomes]
rs16964737	1.00[EUR][1000 genomes]
rs16964750	1.00[EUR][1000 genomes]
rs16964770	1.00[EUR][1000 genomes]
rs2231296	1.00[EUR][1000 genomes]
rs28656256	1.00[EUR][1000 genomes]
rs28663157	1.00[EUR][1000 genomes]
rs41494446	1.00[EUR][1000 genomes]
rs59195841	1.00[EUR][1000 genomes]
rs59289747	1.00[EUR][1000 genomes]
rs7163133	1.00[EUR][1000 genomes]
rs7164357	1.00[EUR][1000 genomes]
rs7165157	1.00[EUR][1000 genomes]
rs7165527	1.00[EUR][1000 genomes]
rs7165708	1.00[EUR][1000 genomes]
rs7167133	1.00[EUR][1000 genomes]
rs7171700	1.00[EUR][1000 genomes]
rs7172939	1.00[EUR][1000 genomes]
rs7178038	1.00[EUR][1000 genomes]
rs730945	1.00[EUR][1000 genomes]
rs73402803	1.00[EUR][1000 genomes]
rs73402816	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs73402824	1.00[EUR][1000 genomes]
rs73402826	1.00[EUR][1000 genomes]
rs73402833	1.00[EUR][1000 genomes]
rs73402839	1.00[EUR][1000 genomes]
rs73402853	1.00[EUR][1000 genomes]
rs73402859	1.00[EUR][1000 genomes]
rs73402869	1.00[EUR][1000 genomes]
rs73402879	1.00[EUR][1000 genomes]
rs73404813	1.00[EUR][1000 genomes]
rs8023921	1.00[EUR][1000 genomes]
rs8024311	1.00[EUR][1000 genomes]
rs8024767	1.00[EUR][1000 genomes]
rs8035146	1.00[EUR][1000 genomes]
rs8040458	1.00[EUR][1000 genomes]
rs8041042	1.00[EUR][1000 genomes]
rs8041128	1.00[EUR][1000 genomes]
rs8041233	1.00[EUR][1000 genomes]
rs8041355	1.00[EUR][1000 genomes]
rs8041504	1.00[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	nsv471244	chr15:52305463-52511465	Enhancers Strong transcription Weak transcription Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
2	nsv984198	chr15:52319726-52481137	Weak transcription Enhancers Genic enhancers ZNF genes & repeats Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
3	nsv1054372	chr15:52369078-52579464	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
4	nsv542387	chr15:52369078-52579464	Enhancers Strong transcription Genic enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
5	nsv833005	chr15:52389869-52541330	Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:51 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:52386200-52399000	Weak transcription	Rectal Smooth Muscle	rectum
2	chr15:52387600-52396600	Weak transcription	Spleen	Spleen
3	chr15:52387600-52396800	Weak transcription	Esophagus	oesophagus
4	chr15:52391800-52397000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr15:52391800-52397000	Enhancers	Muscle Satellite Cultured Cells	--
6	chr15:52392200-52400800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
7	chr15:52392400-52396800	Enhancers	A549	lung
8	chr15:52392400-52397000	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:52392400-52397000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
10	chr15:52392400-52397000	Enhancers	NHDF-Ad	bronchial
11	chr15:52392400-52398600	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:52392600-52396200	Enhancers	Cortex derived primary cultured neurospheres	brain
13	chr15:52392600-52398600	Enhancers	HMEC	breast
14	chr15:52392600-52398600	Enhancers	NHEK	skin
15	chr15:52392800-52396200	Enhancers	HUVEC	blood vessel
16	chr15:52393000-52396800	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
17	chr15:52393000-52397200	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
18	chr15:52393200-52401600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
19	chr15:52393200-52401800	Weak transcription	Pancreas	Pancrea
20	chr15:52393400-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
21	chr15:52394000-52396200	Enhancers	NHLF	lung
22	chr15:52394000-52397800	Enhancers	Primary B cells from peripheral blood	blood
23	chr15:52394200-52396200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:52394200-52396400	Enhancers	NH-A	brain
25	chr15:52394200-52397000	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:52394200-52397400	Enhancers	Primary B cells from cord blood	blood
27	chr15:52394400-52396200	Enhancers	Osteobl	bone
28	chr15:52394600-52396200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr15:52394600-52396800	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
30	chr15:52394600-52397000	Enhancers	HepG2	liver
31	chr15:52395200-52398000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
32	chr15:52395400-52396200	Enhancers	Breast Myoepithelial Primary Cells	Breast
33	chr15:52395400-52396200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
34	chr15:52395400-52396200	Enhancers	Duodenum Smooth Muscle	Duodenum
35	chr15:52395400-52396800	Enhancers	Fetal Adrenal Gland	Adrenal Gland
36	chr15:52395400-52397000	Flanking Active TSS	GM12878-XiMat	blood
37	chr15:52395600-52396800	Weak transcription	Colon Smooth Muscle	Colon
38	chr15:52395600-52397000	Enhancers	Primary hematopoietic stem cells short term culture	blood
39	chr15:52395600-52397000	Enhancers	Adipose Nuclei	Adipose
40	chr15:52395800-52397200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
41	chr15:52395800-52398000	Weak transcription	Brain Cingulate Gyrus	brain
42	chr15:52395800-52398200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
43	chr15:52395800-52401200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
44	chr15:52396000-52396200	Enhancers	Fetal Muscle Trunk	muscle
45	chr15:52396000-52396800	Weak transcription	Brain Germinal Matrix	brain
46	chr15:52396000-52396800	Weak transcription	Skeletal Muscle Male	skeletal muscle
47	chr15:52396000-52397000	Enhancers	Hela-S3	cervix
48	chr15:52396000-52397800	Weak transcription	Brain Hippocampus Middle	brain
49	chr15:52396000-52398000	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:52396000-52401000	Weak transcription	HUES6 Cell Line	embryonic stem cell

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