Variant report

Variant	rs72729404
Chromosome Location	chr15:40077302-40077303
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:14)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:14 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	GATA3	chr15:40076919-40077654	MCF-7	breast:	n/a	n/a
2	FOXM1	chr15:40077078-40077627	MCF-7	breast:	n/a	n/a
3	NR2F2	chr15:40076914-40077764	MCF-7	breast:	n/a	n/a
4	ZNF217	chr15:40076987-40077819	MCF-7	breast:	n/a	n/a
5	NR2F2	chr15:40076886-40077759	MCF-7	breast:	n/a	n/a
6	GATA3	chr15:40076826-40077809	MCF-7	breast:	n/a	n/a
7	CEBPB	chr15:40076905-40077442	MCF-7	breast:	n/a	n/a
8	GATA3	chr15:40076790-40077611	MCF-7	breast:	n/a	n/a
9	TCF7L2	chr15:40077028-40077651	MCF-7	breast:	n/a	n/a
10	HDAC2	chr15:40077058-40077789	MCF-7	breast:	n/a	chr15:40077732-40077746
11	SIN3AK20	chr15:40076895-40077866	MCF-7	breast:	n/a	n/a
12	GATA3	chr15:40076714-40077893	MCF-7	breast:	n/a	n/a
13	SIN3AK20	chr15:40076864-40077878	MCF-7	breast:	n/a	n/a
14	POLR2A	chr15:40077286-40077389	MCF-7	breast:	n/a	n/a

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr15:40071940..40073797-chr15:40075323..40078036,2	MCF-7	breast:
2	chr15:39877336..39879438-chr15:40075503..40079395,4	MCF-7	breast:
3	chr15:40076890..40079993-chr15:40222713..40226528,3	K562	blood:
4	chr15:39960405..39961195-chr15:40076760..40077309,2	MCF-7	breast:
5	chr15:40077135..40079271-chr15:40079393..40081898,2	MCF-7	breast:
6	chr15:39878404..39880564-chr15:40074822..40077432,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-EIF2AK4-4	chr15:40074772-40077818	ENSG00000261136.1
2	lnc-EIF2AK4-4	chr15:40075108-40077815	NONHSAT041769

No data

Variant related genes	Relation type
FSIP1	TF binding region
ENSG00000137801	Chromatin interaction
ENSG00000128829	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs12439384	0.87[EUR][1000 genomes]
rs12591862	1.00[AFR][1000 genomes]
rs1906162	1.00[AFR][1000 genomes]
rs67248221	0.93[EUR][1000 genomes]
rs72727034	1.00[AFR][1000 genomes]
rs72727076	0.83[EUR][1000 genomes]
rs72729408	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs72729424	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs73397128	0.87[EUR][1000 genomes]
rs8182052	0.90[EUR][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	nsv832978	chr15:39899759-40094881	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
2	nsv530816	chr15:40003136-40586792	Bivalent Enhancer Strong transcription Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers ZNF genes & repeats Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv832979	chr15:40041928-40218407	Genic enhancers Weak transcription Enhancers Active TSS ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	21 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:40075600-40078400	Flanking Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:40075800-40077400	Flanking Active TSS	Osteobl	bone
3	chr15:40075800-40077600	Flanking Active TSS	NH-A	brain
4	chr15:40075800-40078400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
5	chr15:40075800-40078600	Weak transcription	Left Ventricle	heart
6	chr15:40075800-40078800	Enhancers	Fetal Brain Male	brain
7	chr15:40075800-40079400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
8	chr15:40075800-40080600	Weak transcription	Placenta Amnion	Placenta Amnion
9	chr15:40076000-40077600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr15:40076000-40077600	Weak transcription	Fetal Lung	lung
11	chr15:40076000-40077800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
12	chr15:40076000-40078000	Weak transcription	Brain Cingulate Gyrus	brain
13	chr15:40076000-40079600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:40076000-40080600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr15:40076000-40081000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr15:40076000-40103200	Weak transcription	Right Atrium	heart
17	chr15:40076200-40077400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr15:40076200-40077400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr15:40076200-40077600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
20	chr15:40076200-40077600	Weak transcription	Fetal Brain Female	brain
21	chr15:40076200-40077800	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr15:40076200-40078800	Enhancers	Cortex derived primary cultured neurospheres	brain
23	chr15:40076200-40079800	Weak transcription	Pancreas	Pancrea
24	chr15:40076200-40080000	Weak transcription	Skeletal Muscle Male	skeletal muscle
25	chr15:40076200-40080800	Weak transcription	Primary B cells from cord blood	blood
26	chr15:40076200-40081400	Weak transcription	Fetal Kidney	kidney
27	chr15:40076400-40077400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
28	chr15:40076400-40077400	Weak transcription	Rectal Mucosa Donor 31	rectum
29	chr15:40076400-40077600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:40076400-40077600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr15:40076400-40077800	Weak transcription	Brain Angular Gyrus	brain
32	chr15:40076400-40078000	Enhancers	Primary T helper cells fromperipheralblood	blood
33	chr15:40076400-40078000	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
34	chr15:40076400-40078000	Enhancers	Dnd41	blood
35	chr15:40076400-40078200	Weak transcription	Brain Hippocampus Middle	brain
36	chr15:40076400-40078600	Weak transcription	Liver	Liver
37	chr15:40076400-40078800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
38	chr15:40076400-40079000	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr15:40076400-40079200	Enhancers	Hela-S3	cervix
40	chr15:40076400-40080600	Weak transcription	Thymus	Thymus
41	chr15:40076600-40077400	Enhancers	ES-I3 Cell Line	embryonic stem cell
42	chr15:40076600-40077400	Weak transcription	HUES6 Cell Line	embryonic stem cell
43	chr15:40076600-40077600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
44	chr15:40076600-40077600	Weak transcription	Brain Anterior Caudate	brain
45	chr15:40076600-40077600	Enhancers	Pancreatic Islets	Pancreatic Islet
46	chr15:40076600-40077800	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
47	chr15:40076600-40077800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
48	chr15:40076600-40077800	Enhancers	NHDF-Ad	bronchial
49	chr15:40076600-40078000	Weak transcription	H9 Cell Line	embryonic stem cell
50	chr15:40076600-40078000	Weak transcription	Brain Inferior Temporal Lobe	brain

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