Variant report

Variant	rs17588
Chromosome Location	chr15:78834533-78834534
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	POLR2A	chr15:78830693-78835554	GM12891	blood:	n/a	n/a
2	POLR2A	chr15:78831504-78834721	MCF10A-Er-Src	breast:	n/a	n/a
3	HCFC1	chr15:78831559-78834951	Hela-S3	cervix:	n/a	n/a
4	IRF1	chr15:78833550-78834632	K562	blood:	n/a	chr15:78833945-78833958 chr15:78833942-78833956 chr15:78833940-78833957 chr15:78833944-78833955 chr15:78833950-78833970 chr15:78834226-78834242 chr15:78833945-78833956 chr15:78833943-78833957 chr15:78833946-78833960 chr15:78833945-78833958 chr15:78833945-78833958 chr15:78833944-78833964 chr15:78833945-78833959 chr15:78833946-78833956

No.	Distal block	Cell Line	Cell type
1	chr15:78831297..78836398-chr15:78856605..78860226,12	MCF-7	breast:
2	chr15:78832604..78836535-chr15:78856473..78859290,6	MCF-7	breast:
3	chr15:78797464..78804546-chr15:78829529..78835433,12	MCF-7	breast:
4	chr15:78834135..78835818-chr15:78847148..78849543,3	K562	blood:
5	chr15:78729933..78731610-chr15:78832734..78835693,2	MCF-7	breast:

Variant related genes	Relation type
PSMA4	TF binding region
ENSG00000169684	Chromatin interaction
ENSG00000136381	Chromatin interaction
ENSG00000188266	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs10450964	1.00[EUR][1000 genomes]
rs10450994	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10450995	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs10851904	1.00[EUR][1000 genomes]
rs10851905	1.00[EUR][1000 genomes]
rs11072773	1.00[EUR][1000 genomes]
rs11855783	1.00[EUR][1000 genomes]
rs11856232	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11856283	1.00[EUR][1000 genomes]
rs11856900	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16969842	1.00[EUR][1000 genomes]
rs16969845	1.00[EUR][1000 genomes]
rs2656068	1.00[EUR][1000 genomes]
rs28820031	1.00[EUR][1000 genomes]
rs34990112	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4887040	1.00[EUR][1000 genomes]
rs4887044	1.00[EUR][1000 genomes]
rs55927929	1.00[EUR][1000 genomes]
rs56182392	1.00[AMR][1000 genomes]
rs56740585	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs56778876	1.00[EUR][1000 genomes]
rs58432603	1.00[EUR][1000 genomes]
rs59046470	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs59098354	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs60507267	1.00[EUR][1000 genomes]
rs61208420	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs61695517	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs73467242	1.00[EUR][1000 genomes]
rs73467244	1.00[EUR][1000 genomes]
rs73467262	1.00[EUR][1000 genomes]
rs73467265	1.00[EUR][1000 genomes]
rs73467279	1.00[EUR][1000 genomes]
rs74024421	1.00[EUR][1000 genomes]
rs9920382	1.00[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv917303	chr15:78491050-79205255	Enhancers Genic enhancers Weak transcription Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	122 gene(s)	inside rSNPs	diseases
2	nsv1038816	chr15:78796434-78881087	Strong transcription Enhancers Bivalent/Poised TSS Weak transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region	48 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:127 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:78832000-78834600	Active TSS	Colonic Mucosa	Colon
2	chr15:78832200-78834600	Active TSS	Psoas Muscle	Psoas
3	chr15:78832200-78834600	Active TSS	Right Atrium	heart
4	chr15:78832200-78834600	Active TSS	NHLF	lung
5	chr15:78832400-78834800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
6	chr15:78832400-78834800	Active TSS	GM12878-XiMat	blood
7	chr15:78833200-78834600	Flanking Active TSS	Primary B cells from cord blood	blood
8	chr15:78833200-78834600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr15:78833200-78834600	Flanking Active TSS	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr15:78833400-78834600	Flanking Active TSS	Primary T killer naive cells fromperipheralblood	blood
11	chr15:78833400-78834600	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
12	chr15:78833400-78834600	Flanking Active TSS	Brain Germinal Matrix	brain
13	chr15:78833600-78834600	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
14	chr15:78833600-78834600	Flanking Active TSS	HUVEC	blood vessel
15	chr15:78833600-78834600	Flanking Active TSS	Osteobl	bone
16	chr15:78833600-78838400	Weak transcription	Spleen	Spleen
17	chr15:78833800-78834600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
18	chr15:78833800-78834600	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
19	chr15:78833800-78834600	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
20	chr15:78833800-78834600	Enhancers	Brain Substantia Nigra	brain
21	chr15:78833800-78834800	Weak transcription	Lung	lung
22	chr15:78833800-78835200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
23	chr15:78833800-78835400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr15:78833800-78835600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:78833800-78837800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
26	chr15:78833800-78838000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
27	chr15:78833800-78838000	Weak transcription	Esophagus	oesophagus
28	chr15:78833800-78838000	Weak transcription	Gastric	stomach
29	chr15:78833800-78838400	Weak transcription	Pancreas	Pancrea
30	chr15:78834000-78834600	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
31	chr15:78834000-78834600	Flanking Active TSS	Duodenum Smooth Muscle	Duodenum
32	chr15:78834000-78834600	Enhancers	Fetal Brain Male	brain
33	chr15:78834000-78834600	Weak transcription	Left Ventricle	heart
34	chr15:78834000-78834600	Flanking Active TSS	HepG2	liver
35	chr15:78834000-78834600	Flanking Active TSS	NHDF-Ad	bronchial
36	chr15:78834000-78834800	Flanking Active TSS	HMEC	breast
37	chr15:78834000-78835000	Weak transcription	Fetal Kidney	kidney
38	chr15:78834000-78835000	Weak transcription	Placenta Amnion	Placenta Amnion
39	chr15:78834000-78835000	Weak transcription	Right Ventricle	heart
40	chr15:78834000-78835000	Weak transcription	Sigmoid Colon	Sigmoid Colon
41	chr15:78834000-78835000	Transcr. at gene 5' and 3'	A549	lung
42	chr15:78834000-78835600	Weak transcription	Aorta	Aorta
43	chr15:78834000-78837600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
44	chr15:78834000-78838000	Weak transcription	Small Intestine	intestine
45	chr15:78834200-78834600	Enhancers	H1 Cell Line	embryonic stem cell
46	chr15:78834200-78834600	Transcr. at gene 5' and 3'	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr15:78834200-78834600	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr15:78834200-78834600	Weak transcription	Primary T cells fromperipheralblood	blood
49	chr15:78834200-78834600	Weak transcription	Primary hematopoietic stem cells	blood
50	chr15:78834200-78834600	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--

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