Variant report

Variant	rs353099
Chromosome Location	chr15:45924015-45924016
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	chr15:45923507-45924108	HCT-116	colon:	n/a	n/a
2	ELF1	chr15:45923504-45924377	HCT-116	colon:	n/a	n/a
3	GABPA	chr15:45923633-45924109	A549	lung:	n/a	n/a
4	SPI1	chr15:45923804-45924236	HL-60	blood:	n/a	n/a
5	POLR2A	chr15:45923324-45924366	U87	brain:	n/a	n/a
6	MAZ	chr15:45923623-45924126	Hela-S3	cervix:	n/a	chr15:45923903-45923914
7	POLR2A	chr15:45923378-45924372	U87	brain:	n/a	n/a
8	MAX	chr15:45923647-45924146	A549	lung:	n/a	chr15:45923903-45923914
9	MAFK	chr15:45923511-45924106	IMR90	lung:	n/a	n/a
10	POLR2A	chr15:45923461-45924360	U87	brain:	n/a	n/a
11	FOS	chr15:45923529-45924343	MCF10A-Er-Src	breast:	n/a	chr15:45924208-45924215
12	FOS	chr15:45923589-45924384	MCF10A-Er-Src	breast:	n/a	chr15:45924208-45924215
13	POLR2A	chr15:45923526-45924026	ProgFib	skin:	n/a	n/a
14	POLR2A	chr15:45923444-45924360	U87	brain:	n/a	n/a
15	POLR2A	chr15:45923492-45924198	HCT-116	colon:	n/a	n/a
16	SPI1	chr15:45923654-45924345	HL-60	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr15:45923721..45925487-chr15:45925745..45928411,3	MCF-7	breast:
2	chr15:45877501..45879866-chr15:45923125..45926614,3	MCF-7	breast:
3	chr15:45922262..45924603-chr15:45925302..45927277,3	MCF-7	breast:
4	chr15:45859095..45860936-chr15:45923807..45926477,2	K562	blood:

Variant related genes	Relation type
SQRDL	TF binding region
ENSG00000137767	Chromatin interaction
ENSG00000104164	Chromatin interaction
ENSG00000260170	Chromatin interaction

Extended variants
information (count: 17 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11632553	0.89[CEU][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637892	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11637946	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11637984	0.89[CEU][hapmap];0.95[MEX][hapmap];0.83[TSI][hapmap];0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs12440208	0.85[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs187095	0.99[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2733246	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3985920	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs625047	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs6493164	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs66808613	0.87[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs8039784	0.89[CEU][hapmap];0.85[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs8043334	0.81[CEU][hapmap]

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:4)

SNP	Gene	Cis/trans	Tissue	Source
rs353099	RPAP1	cis	cerebellum	SCAN
rs353099	GPR176	cis	cerebellum	SCAN
rs353099	SQRDL	Cis_1M	lymphoblastoid	RTeQTL
rs353099	SLC30A4	cis	parietal	SCAN

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:45909600-45926600	Weak transcription	Sigmoid Colon	Sigmoid Colon
2	chr15:45923000-45925400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr15:45923400-45924200	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
4	chr15:45923600-45924200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr15:45923600-45924200	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr15:45923600-45924200	Flanking Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:45923600-45924200	Enhancers	Primary hematopoietic stem cells short term culture	blood
8	chr15:45923600-45924200	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr15:45923600-45924200	Flanking Active TSS	Muscle Satellite Cultured Cells	--
10	chr15:45923600-45924200	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
11	chr15:45923600-45924200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
12	chr15:45923600-45924200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
13	chr15:45923600-45924200	Flanking Active TSS	Adipose Nuclei	Adipose
14	chr15:45923600-45924200	Enhancers	Fetal Intestine Small	intestine
15	chr15:45923600-45924200	Bivalent Enhancer	Fetal Muscle Leg	muscle
16	chr15:45923600-45924200	Enhancers	Gastric	stomach
17	chr15:45923600-45924200	Enhancers	Lung	lung
18	chr15:45923600-45924200	Enhancers	Psoas Muscle	Psoas
19	chr15:45923600-45924200	Flanking Active TSS	Rectal Mucosa Donor 29	rectum
20	chr15:45923600-45924200	Flanking Active TSS	Rectal Mucosa Donor 31	rectum
21	chr15:45923600-45924200	Active TSS	Rectal Smooth Muscle	rectum
22	chr15:45923600-45924200	Active TSS	Stomach Smooth Muscle	stomach
23	chr15:45923600-45924200	Flanking Active TSS	GM12878-XiMat	blood
24	chr15:45923600-45924200	Flanking Active TSS	Hela-S3	cervix
25	chr15:45923600-45924200	Flanking Active TSS	HSMM	muscle
26	chr15:45923600-45924200	Flanking Active TSS	HSMMtube	muscle
27	chr15:45923600-45924200	Enhancers	HUVEC	blood vessel
28	chr15:45923600-45924200	Flanking Active TSS	NH-A	brain
29	chr15:45923600-45924200	Flanking Active TSS	Osteobl	bone
30	chr15:45923600-45924400	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
31	chr15:45923600-45924400	Flanking Active TSS	Primary monocytes fromperipheralblood	blood
32	chr15:45923600-45924400	Flanking Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
33	chr15:45923600-45924400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
34	chr15:45923600-45924400	Flanking Active TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
35	chr15:45923600-45924400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
36	chr15:45923600-45924400	Flanking Active TSS	NHDF-Ad	bronchial
37	chr15:45923600-45924400	Flanking Active TSS	NHEK	skin
38	chr15:45923800-45924200	Flanking Active TSS	ES-I3 Cell Line	embryonic stem cell
39	chr15:45923800-45924200	Active TSS	Duodenum Mucosa	Duodenum
40	chr15:45923800-45924200	Active TSS	Fetal Kidney	kidney
41	chr15:45923800-45924200	Flanking Active TSS	A549	lung
42	chr15:45923800-45924200	Flanking Active TSS	HMEC	breast
43	chr15:45923800-45924200	Flanking Active TSS	NHLF	lung
44	chr15:45923800-45926600	Weak transcription	Right Ventricle	heart
45	chr15:45924000-45924200	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
46	chr15:45924000-45924200	Enhancers	Primary T helper cells PMA-I stimulated	--
47	chr15:45924000-45924200	Flanking Active TSS	Colon Smooth Muscle	Colon
48	chr15:45924000-45924400	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
49	chr15:45924000-45926400	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr15:45924000-45926400	Weak transcription	Fetal Intestine Large	intestine

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