Variant report

Variant	rs7224619
Chromosome Location	chr17:17572384-17572385
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr17:17565443..17568404-chr17:17572179..17574047,2	MCF-7	breast:
2	chr17:17571014..17573975-chr17:17596687..17598856,2	K562	blood:

Extended variants
information (count: 38 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs12936277	0.90[ASN][1000 genomes]
rs12940014	0.88[CEU][hapmap];0.93[TSI][hapmap];0.87[EUR][1000 genomes]
rs2001884	0.81[CEU][hapmap];0.80[EUR][1000 genomes]
rs2350632	0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2350633	0.82[EUR][1000 genomes]
rs4496218	0.88[CEU][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.95[TSI][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs4924807	0.84[EUR][1000 genomes]
rs4925092	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.93[YRI][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925093	0.83[ASW][hapmap];1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[YRI][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925094	1.00[CEU][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4925095	0.84[EUR][1000 genomes]
rs4925096	0.81[AFR][1000 genomes];0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4925102	0.89[EUR][1000 genomes]
rs4925104	0.88[CEU][hapmap];0.86[EUR][1000 genomes]
rs4925105	0.88[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs6502613	0.89[CEU][hapmap];0.87[TSI][hapmap];0.85[EUR][1000 genomes]
rs6502615	0.85[CEU][hapmap]
rs7208561	0.82[CEU][hapmap]
rs7214245	0.85[EUR][1000 genomes]
rs7224617	0.88[CEU][hapmap];0.91[TSI][hapmap];0.87[EUR][1000 genomes]
rs7224739	0.81[CEU][hapmap]
rs7225934	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs8065154	0.85[CEU][hapmap]
rs8075153	0.85[CEU][hapmap]
rs897457	0.96[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs9897044	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9897309	0.88[CEU][hapmap];0.91[TSI][hapmap];0.86[EUR][1000 genomes]
rs9897596	0.89[EUR][1000 genomes]
rs9904468	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9906532	0.85[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv907748	chr17:17412032-17782404	Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
2	nsv1065270	chr17:17430116-17823086	Weak transcription Flanking Active TSS Genic enhancers Enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
3	nsv543236	chr17:17430116-17823086	Bivalent Enhancer Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
4	nsv833384	chr17:17491483-17645648	Flanking Active TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
5	nsv869118	chr17:17509896-17599850	Active TSS Weak transcription Enhancers Flanking Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv907751	chr17:17530554-17581184	Enhancers Weak transcription Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
7	nsv907752	chr17:17569012-17750907	Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	77 gene(s)	inside rSNPs	diseases
8	nsv531183	chr17:17571035-18205309	Genic enhancers Weak transcription Enhancers Strong transcription Active TSS Flanking 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 miRNA target site	123 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs7224619	SREBF1	cis	cerebellum	SCAN
rs7224619	TOM1L2	cis	parietal	SCAN
rs7224619	FAM106A	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:17567000-17572400	Weak transcription	Brain Inferior Temporal Lobe	brain
2	chr17:17567000-17573200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
3	chr17:17567200-17572400	Weak transcription	Fetal Brain Male	brain
4	chr17:17567200-17572600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr17:17567200-17572600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr17:17567200-17574400	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr17:17567200-17575400	Weak transcription	Primary hematopoietic stem cells	blood
8	chr17:17567200-17579200	Weak transcription	K562	blood
9	chr17:17567400-17572400	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr17:17567400-17575400	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr17:17568200-17573800	Weak transcription	Left Ventricle	heart
12	chr17:17568200-17576200	Weak transcription	Spleen	Spleen
13	chr17:17568800-17574000	Enhancers	Fetal Thymus	thymus
14	chr17:17569000-17575600	Weak transcription	GM12878-XiMat	blood
15	chr17:17569400-17572600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr17:17569400-17572800	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
17	chr17:17569400-17572800	Enhancers	HMEC	breast
18	chr17:17570000-17576000	Weak transcription	Right Ventricle	heart
19	chr17:17570200-17575600	Weak transcription	Hela-S3	cervix
20	chr17:17570800-17572600	Weak transcription	Pancreas	Pancrea
21	chr17:17570800-17572600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr17:17570800-17574000	Enhancers	HepG2	liver
23	chr17:17570800-17574600	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr17:17571000-17575600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr17:17571200-17572600	Bivalent Enhancer	Fetal Muscle Trunk	muscle
26	chr17:17571400-17573000	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr17:17571400-17574400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
28	chr17:17571600-17573800	Enhancers	Thymus	Thymus
29	chr17:17571800-17572400	Bivalent Enhancer	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr17:17571800-17572600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
31	chr17:17571800-17574600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr17:17572000-17572400	Enhancers	HSMMtube	muscle
33	chr17:17572000-17572600	Enhancers	HSMM	muscle
34	chr17:17572000-17573200	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
35	chr17:17572000-17573400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
36	chr17:17572200-17572400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr17:17572200-17572400	Enhancers	Gastric	stomach
38	chr17:17572200-17572600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
39	chr17:17572200-17572600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
40	chr17:17572200-17572600	Enhancers	Muscle Satellite Cultured Cells	--
41	chr17:17572200-17572600	Enhancers	NH-A	brain
42	chr17:17572200-17572800	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
43	chr17:17572200-17572800	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr17:17572200-17572800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
45	chr17:17572200-17573000	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr17:17572200-17573400	Enhancers	Cortex derived primary cultured neurospheres	brain
47	chr17:17572200-17573600	Enhancers	Fetal Brain Female	brain
48	chr17:17572200-17574200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr17:17572200-17577600	Enhancers	Fetal Heart	heart

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