Variant report

Variant	rs625466
Chromosome Location	chr15:45933179-45933180
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	SP1	chr15:45932682-45933263	HCT-116	colon:	n/a	n/a
2	FOSL2	chr15:45932814-45933219	HepG2	liver:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933031-45933042
3	CBX3	chr15:45932687-45933203	HCT-116	colon:	n/a	n/a
4	TCF12	chr15:45932662-45934664	A549	lung:	n/a	n/a
5	JUN	chr15:45932791-45933189	HUVEC	blood vessel:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933031-45933042
6	MAX	chr15:45932735-45933187	A549	lung:	n/a	n/a
7	POLR2A	chr15:45932693-45934852	MCF10A-Er-Src	breast:	n/a	n/a
8	ARID3A	chr15:45933053-45934166	HepG2	liver:	n/a	n/a
9	JUND	chr15:45932792-45933272	HCT-116	colon:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933033-45933044 chr15:45933031-45933042
10	FOSL2	chr15:45932753-45933242	SK-N-SH	brain:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933031-45933042
11	STAT3	chr15:45932723-45933247	MCF10A-Er-Src	breast:	n/a	chr15:45933087-45933098
12	JUND	chr15:45932806-45933221	A549	lung:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933033-45933044 chr15:45933031-45933042
13	FOS	chr15:45932745-45934821	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
14	JUND	chr15:45932726-45933301	HCT-116	colon:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933033-45933044 chr15:45933031-45933042
15	NR3C1	chr15:45932835-45933205	A549	lung:	n/a	n/a
16	FOS	chr15:45932705-45934919	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
17	FOSL1	chr15:45932839-45933236	HCT-116	colon:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933031-45933042
18	SP1	chr15:45932728-45933277	A549	lung:	n/a	n/a
19	FOS	chr15:45932668-45934971	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
20	STAT3	chr15:45932629-45934910	MCF10A-Er-Src	breast:	n/a	chr15:45933849-45933857 chr15:45933314-45933323 chr15:45933976-45933984 chr15:45933087-45933098 chr15:45933313-45933322 chr15:45933545-45933553
21	SP1	chr15:45932707-45933247	HCT-116	colon:	n/a	n/a
22	POLR2A	chr15:45932657-45934590	MCF10A-Er-Src	breast:	n/a	n/a
23	FOSL2	chr15:45932624-45934799	A549	lung:	n/a	chr15:45933034-45933043 chr15:45933649-45933660 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933031-45933042
24	SP1	chr15:45932767-45933257	A549	lung:	n/a	n/a
25	NR3C1	chr15:45932840-45933227	A549	lung:	n/a	n/a
26	POLR2A	chr15:45932737-45933231	Hela-S3	cervix:	n/a	n/a
27	FOXA2	chr15:45932857-45933256	A549	lung:	n/a	n/a
28	JUND	chr15:45932828-45933253	MCF-7	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933033-45933044 chr15:45933031-45933042
29	E2F4	chr15:45932896-45933247	MCF10A-Er-Src	breast:	n/a	n/a
30	GATA3	chr15:45932707-45934225	A549	lung:	n/a	chr15:45933653-45933662
31	MAX	chr15:45932672-45933245	A549	lung:	n/a	n/a
32	FOS	chr15:45932748-45934071	MCF10A-Er-Src	breast:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042
33	MYC	chr15:45932646-45933207	MCF10A-Er-Src	breast:	n/a	n/a
34	STAT3	chr15:45932737-45933250	MCF10A-Er-Src	breast:	n/a	chr15:45933087-45933098
35	MYC	chr15:45932756-45933181	MCF10A-Er-Src	breast:	n/a	n/a
36	FOSL1	chr15:45932668-45933264	HCT-116	colon:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933031-45933042
37	TCF12	chr15:45932759-45933356	SK-N-SH	brain:	n/a	n/a
38	FOS	chr15:45932759-45933982	HUVEC	blood vessel:	n/a	chr15:45933034-45933043 chr15:45933036-45933043 chr15:45933652-45933660 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933034-45933044 chr15:45933033-45933044 chr15:45933651-45933661 chr15:45933651-45933661 chr15:45933033-45933044 chr15:45933031-45933042

No.	Distal block	Cell Line	Cell type
1	chr15:45933052..45935436-chr15:45937380..45939217,2	K562	blood:
2	chr15:45931689..45934379-chr15:45936432..45937938,2	MCF-7	breast:
3	chr15:45932766..45934482-chr15:45951327..45953164,2	MCF-7	breast:
4	chr15:45931592..45934146-chr15:45938709..45942844,4	MCF-7	breast:

Variant related genes	Relation type
SQRDL	TF binding region
ENSG00000137767	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs11632130	0.98[AMR][1000 genomes];0.90[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11633216	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442114	1.00[CEU][hapmap];0.86[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.89[TSI][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1967502	1.00[CEU][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2899382	0.87[GIH][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs34311210	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs353095	1.00[YRI][hapmap]
rs353106	0.89[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3985921	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3985922	0.86[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs594516	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.84[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs612451	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs629986	1.00[YRI][hapmap];0.81[AFR][1000 genomes]
rs636992	0.82[YRI][hapmap]
rs6493165	0.94[MEX][hapmap];0.82[TSI][hapmap];0.84[AMR][1000 genomes]
rs7174285	0.80[EUR][1000 genomes]
rs8026123	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8026175	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040662	1.00[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs8040706	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[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	nsv904188	chr15:45801035-45941689	Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Weak transcription Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	57 gene(s)	inside rSNPs	diseases
2	nsv904189	chr15:45821158-46298458	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv904190	chr15:45892672-45960897	Enhancers Weak transcription Strong transcription Flanking Active TSS Bivalent/Poised TSS Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region miRNA target site	27 gene(s)	inside rSNPs	n/a
4	nsv904191	chr15:45902779-46381874	Flanking Active TSS Bivalent Enhancer Weak transcription Enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Strong transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs625466	SQRDL	cis	lymphoblastoid	seeQTL
rs625466	SQRDL	cis	multi-tissue	Pritchard

Chromatin state (count:94 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45927800-45935400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
2	chr15:45928200-45934200	Weak transcription	Ovary	ovary
3	chr15:45929000-45939000	Enhancers	Stomach Mucosa	stomach
4	chr15:45929800-45934000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr15:45930000-45933200	Enhancers	Esophagus	oesophagus
6	chr15:45930000-45934200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
7	chr15:45930000-45937800	Weak transcription	Right Ventricle	heart
8	chr15:45930200-45933400	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
9	chr15:45930200-45933400	Weak transcription	Brain Angular Gyrus	brain
10	chr15:45930200-45933400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
11	chr15:45930200-45933600	Weak transcription	Brain Substantia Nigra	brain
12	chr15:45930200-45933800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
13	chr15:45930200-45933800	Weak transcription	Fetal Kidney	kidney
14	chr15:45930200-45933800	Weak transcription	Fetal Lung	lung
15	chr15:45930200-45934200	Weak transcription	Brain Anterior Caudate	brain
16	chr15:45930200-45935800	Enhancers	Fetal Intestine Large	intestine
17	chr15:45930400-45933200	Enhancers	Sigmoid Colon	Sigmoid Colon
18	chr15:45930400-45933600	Enhancers	Skeletal Muscle Female	skeletal muscle
19	chr15:45930400-45935200	Enhancers	Colon Smooth Muscle	Colon
20	chr15:45930400-45935400	Enhancers	Fetal Intestine Small	intestine
21	chr15:45930400-45936800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
22	chr15:45930400-45940800	Weak transcription	Fetal Thymus	thymus
23	chr15:45930600-45933600	Weak transcription	Brain Hippocampus Middle	brain
24	chr15:45930600-45934000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
25	chr15:45930600-45934000	Enhancers	NHLF	lung
26	chr15:45930600-45934200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
27	chr15:45930600-45934200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr15:45930600-45934200	Enhancers	Colonic Mucosa	Colon
29	chr15:45930600-45934800	Enhancers	Small Intestine	intestine
30	chr15:45930600-45940800	Weak transcription	Thymus	Thymus
31	chr15:45930800-45933800	Weak transcription	Placenta	Placenta
32	chr15:45930800-45936800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr15:45931000-45933800	Genic enhancers	Primary B cells from cord blood	blood
34	chr15:45931000-45936600	Weak transcription	Primary T helper naive cells from peripheral blood	blood
35	chr15:45931000-45938800	Enhancers	Primary monocytes fromperipheralblood	blood
36	chr15:45931200-45933600	Weak transcription	Primary hematopoietic stem cells short term culture	blood
37	chr15:45931200-45934200	Weak transcription	Lung	lung
38	chr15:45931600-45933400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
39	chr15:45931600-45933800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr15:45931600-45933800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr15:45931600-45934000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
42	chr15:45931600-45936600	Weak transcription	Primary B cells from peripheral blood	blood
43	chr15:45931800-45933200	Strong transcription	Primary T cells from cord blood	blood
44	chr15:45931800-45933200	Enhancers	NHDF-Ad	bronchial
45	chr15:45931800-45933400	Enhancers	Liver	Liver
46	chr15:45931800-45933600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
47	chr15:45931800-45933600	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
48	chr15:45931800-45934200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
49	chr15:45931800-45934200	Weak transcription	Aorta	Aorta
50	chr15:45932000-45933200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell

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