Variant report

Variant	rs7515895
Chromosome Location	chr1:172416860-172416861
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	STAT3	chr1:172416743-172417063	MCF10A-Er-Src	breast:	n/a	chr1:172416908-172416919 chr1:172416880-172416891
2	E2F4	chr1:172416839-172417036	MCF10A-Er-Src	breast:	n/a	chr1:172416882-172416896
3	SPI1	chr1:172416635-172417356	HL-60	blood:	n/a	n/a
4	FOS	chr1:172416734-172417197	MCF10A-Er-Src	breast:	n/a	n/a
5	MYC	chr1:172416635-172417148	MCF10A-Er-Src	breast:	n/a	n/a
6	GATA1	chr1:172416667-172417261	PBDE	blood:	n/a	chr1:172417118-172417128
7	STAT3	chr1:172416656-172417137	MCF10A-Er-Src	breast:	n/a	chr1:172416908-172416919 chr1:172416880-172416891
8	POLR2A	chr1:172416647-172416900	MCF10A-Er-Src	breast:	n/a	n/a
9	MYC	chr1:172416742-172417202	MCF10A-Er-Src	breast:	n/a	n/a
10	FOS	chr1:172416758-172417103	MCF10A-Er-Src	breast:	n/a	n/a
11	STAT3	chr1:172416737-172417050	MCF10A-Er-Src	breast:	n/a	chr1:172416908-172416919 chr1:172416880-172416891
12	FOS	chr1:172416763-172417158	MCF10A-Er-Src	breast:	n/a	n/a
13	POLR2A	chr1:172416710-172417378	HL-60	blood:	n/a	n/a
14	SPI1	chr1:172416828-172417211	HL-60	blood:	n/a	n/a
15	CEBPB	chr1:172416700-172417283	MCF-7	breast:	n/a	chr1:172416937-172416950 chr1:172416936-172416953
16	STAT3	chr1:172416716-172417300	MCF10A-Er-Src	breast:	n/a	chr1:172416908-172416919 chr1:172416880-172416891
17	REST	chr1:172416687-172417636	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr1:172416555..172419141-chr1:172466431..172468171,3	MCF-7	breast:
2	chr1:172416845..172420491-chr1:172421660..172424212,3	MCF-7	breast:
3	chr1:172416738..172419262-chr1:172481149..172482659,2	MCF-7	breast:
4	chr1:172411084..172422561-chr1:172496524..172504623,44	MCF-7	breast:
5	chr1:172412087..172424934-chr1:172497120..172505334,59	MCF-7	breast:

Variant related genes	Relation type
PIGC	TF binding region
C1orf105	TF binding region
ENSG00000180999	Chromatin interaction
ENSG00000094975	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:26)

rs_ID	r²[population]
rs1009802	1.00[CHD][hapmap]
rs1129942	0.89[EUR][1000 genomes]
rs16844417	1.00[CHD][hapmap]
rs17278379	1.00[CHD][hapmap]
rs17369123	0.84[CEU][hapmap]
rs2001130	0.89[EUR][1000 genomes]
rs2001132	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs2213738	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.84[MEX][hapmap];0.89[EUR][1000 genomes]
rs2901655	0.89[EUR][1000 genomes]
rs3948765	0.89[EUR][1000 genomes]
rs4244193	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs4244194	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs4916187	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs4916260	0.89[EUR][1000 genomes]
rs4916261	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs6660798	0.83[EUR][1000 genomes]
rs6689291	0.90[EUR][1000 genomes]
rs739249	1.00[CEU][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[MEX][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7518300	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs7522692	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs7538417	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.92[MEX][hapmap];0.89[EUR][1000 genomes]
rs7544376	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7551242	1.00[CHD][hapmap]
rs9425328	0.89[EUR][1000 genomes]
rs9425330	1.00[CEU][hapmap];1.00[CHD][hapmap];0.90[GIH][hapmap];0.89[EUR][1000 genomes]
rs9425620	0.89[EUR][1000 genomes]

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs7515895	VAMP4	cis	cerebellum	SCAN
rs7515895	GPA33	cis	parietal	SCAN

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:172413600-172417200	Weak transcription	NHEK	skin
2	chr1:172413600-172417600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
3	chr1:172413600-172417800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr1:172413600-172417800	Weak transcription	Placenta	Placenta
5	chr1:172413600-172418000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr1:172413600-172418000	Weak transcription	HSMMtube	muscle
7	chr1:172413600-172418000	Weak transcription	NH-A	brain
8	chr1:172413600-172418400	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr1:172413600-172418600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr1:172413600-172418600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr1:172413600-172418600	Weak transcription	Esophagus	oesophagus
12	chr1:172413600-172418800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
13	chr1:172413600-172418800	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
14	chr1:172413600-172418800	Weak transcription	Fetal Muscle Trunk	muscle
15	chr1:172413600-172418800	Weak transcription	Lung	lung
16	chr1:172413600-172418800	Weak transcription	Small Intestine	intestine
17	chr1:172413600-172419000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:172413600-172419000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
19	chr1:172413600-172419000	Weak transcription	Fetal Thymus	thymus
20	chr1:172413600-172419000	Weak transcription	Right Ventricle	heart
21	chr1:172413600-172419200	Weak transcription	Fetal Heart	heart
22	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
23	chr1:172413600-172421800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr1:172413800-172417200	Weak transcription	Pancreatic Islets	Pancreatic Islet
25	chr1:172413800-172417800	Weak transcription	Duodenum Mucosa	Duodenum
26	chr1:172413800-172417800	Weak transcription	Fetal Kidney	kidney
27	chr1:172413800-172418200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr1:172413800-172418200	Weak transcription	K562	blood
29	chr1:172413800-172418800	Weak transcription	HUES6 Cell Line	embryonic stem cell
30	chr1:172413800-172418800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
31	chr1:172413800-172418800	Weak transcription	Duodenum Smooth Muscle	Duodenum
32	chr1:172413800-172418800	Weak transcription	GM12878-XiMat	blood
33	chr1:172413800-172419000	Weak transcription	Primary B cells from peripheral blood	blood
34	chr1:172413800-172419000	Weak transcription	Primary T cells from cord blood	blood
35	chr1:172413800-172419000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr1:172413800-172419000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
37	chr1:172413800-172419000	Weak transcription	Liver	Liver
38	chr1:172413800-172419000	Weak transcription	Brain Anterior Caudate	brain
39	chr1:172413800-172419000	Weak transcription	Brain Hippocampus Middle	brain
40	chr1:172413800-172419000	Weak transcription	Brain Substantia Nigra	brain
41	chr1:172413800-172419000	Weak transcription	Rectal Mucosa Donor 29	rectum
42	chr1:172413800-172419400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
43	chr1:172413800-172419400	Weak transcription	NHDF-Ad	bronchial
44	chr1:172414000-172417200	Weak transcription	A549	lung
45	chr1:172414000-172418400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
46	chr1:172414000-172418800	Weak transcription	Primary B cells from cord blood	blood
47	chr1:172414000-172418800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
48	chr1:172414000-172418800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
49	chr1:172414000-172418800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
50	chr1:172414000-172419000	Weak transcription	Primary T helper cells PMA-I stimulated	--

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