Variant report

Variant	rs1299684
Chromosome Location	chr1:179799430-179799431
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr1:179799294..179801607-chr1:179806721..179809341,2	MCF-7	breast:
2	chr1:179793280..179795680-chr1:179799049..179800852,2	K562	blood:
3	chr1:179798950..179801590-chr1:179923163..179925286,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000260360	Chromatin interaction
ENSG00000135837	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:14)

rs_ID	r²[population]
rs1014394	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs1148820	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1148821	0.85[AFR][1000 genomes];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2252288	0.94[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2252384	0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2252388	0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2777912	0.80[ASN][1000 genomes]
rs2777913	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.83[TSI][hapmap];0.92[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2777914	0.96[CEU][hapmap];0.84[MEX][hapmap];0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2777915	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2794579	0.96[CEU][hapmap];0.83[JPT][hapmap];0.89[MEX][hapmap];0.86[TSI][hapmap];0.93[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs518774	0.81[YRI][hapmap]
rs555270	0.81[YRI][hapmap]
rs589780	0.81[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1011407	chr1:179733193-179799430	Bivalent Enhancer Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
2	nsv1005808	chr1:179783922-179864710	Enhancers Strong transcription Weak transcription Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
3	nsv1005051	chr1:179785643-179861950	Flanking Active TSS Strong transcription Genic enhancers Weak transcription Enhancers Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	40 gene(s)	inside rSNPs	diseases
4	nsv429936	chr1:179790343-180214343	Active TSS Strong transcription Flanking Active TSS Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	72 gene(s)	inside rSNPs	diseases
5	nsv429947	chr1:179790518-179925104	Strong transcription Enhancers Genic enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	49 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1299684	ANGPTL1	cis	cerebellum	SCAN

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:179791000-179807200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr1:179793800-179808800	Weak transcription	Monocytes-CD14+_RO01746	blood
3	chr1:179794600-179804800	Weak transcription	Right Ventricle	heart
4	chr1:179794800-179809200	Weak transcription	Skeletal Muscle Male	skeletal muscle
5	chr1:179795200-179812400	Weak transcription	Left Ventricle	heart
6	chr1:179795200-179815200	Weak transcription	Ovary	ovary
7	chr1:179795400-179804600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
8	chr1:179795400-179804800	Weak transcription	Skeletal Muscle Female	skeletal muscle
9	chr1:179795400-179805000	Weak transcription	Fetal Muscle Leg	muscle
10	chr1:179795400-179807600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr1:179795400-179815200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
12	chr1:179795600-179800800	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr1:179795600-179834200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
14	chr1:179796000-179799800	Weak transcription	Fetal Thymus	thymus
15	chr1:179796000-179800600	Weak transcription	Spleen	Spleen
16	chr1:179796000-179800800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:179797400-179805800	Weak transcription	Primary monocytes fromperipheralblood	blood
18	chr1:179797600-179810000	Weak transcription	Primary neutrophils fromperipheralblood	blood
19	chr1:179798400-179802400	Weak transcription	Placenta	Placenta
20	chr1:179798400-179805800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
21	chr1:179799200-179800200	Enhancers	Primary T helper naive cells fromperipheralblood	blood
22	chr1:179799200-179800600	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr1:179799400-179800600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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