Variant report

Variant	rs2176862
Chromosome Location	chr3:46650993-46650994
allele	A/G
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	EP300	chr3:46650749-46651011	Hela-S3	cervix:	n/a	n/a
2	TCF7L2	chr3:46650930-46651242	Hela-S3	cervix:	n/a	n/a
3	CEBPB	chr3:46650819-46651132	IMR90	lung:	n/a	chr3:46650974-46650985 chr3:46650973-46650986
4	CEBPB	chr3:46650783-46651144	Hela-S3	cervix:	n/a	chr3:46650974-46650985 chr3:46650973-46650986
5	STAT3	chr3:46650805-46651125	MCF10A-Er-Src	breast:	n/a	chr3:46650885-46650896
6	CHD2	chr3:46650817-46651029	Hela-S3	cervix:	n/a	n/a
7	E2F6	chr3:46650875-46651321	H1-hESC	embryonic stem cell:	n/a	n/a
8	STAT3	chr3:46650661-46651111	Hela-S3	cervix:	n/a	chr3:46650885-46650896
9	STAT3	chr3:46650766-46651045	MCF10A-Er-Src	breast:	n/a	chr3:46650885-46650896
10	CEBPB	chr3:46650828-46651092	HepG2	liver:	n/a	chr3:46650974-46650985 chr3:46650973-46650986
11	MAX	chr3:46650990-46651190	H1-hESC	embryonic stem cell:	n/a	n/a
12	CEBPB	chr3:46650853-46651103	K562	blood:	n/a	chr3:46650974-46650985 chr3:46650973-46650986
13	MAZ	chr3:46650833-46651126	Hela-S3	cervix:	n/a	n/a
14	E2F6	chr3:46650760-46651328	H1-hESC	embryonic stem cell:	n/a	n/a
15	MAX	chr3:46650722-46651165	Hela-S3	cervix:	n/a	n/a
16	STAT3	chr3:46650712-46651093	MCF10A-Er-Src	breast:	n/a	chr3:46650885-46650896
17	PRDM1	chr3:46650653-46651049	Hela-S3	cervix:	n/a	chr3:46650883-46650898 chr3:46650888-46650897 chr3:46650884-46650898
18	STAT3	chr3:46650769-46651021	MCF10A-Er-Src	breast:	n/a	chr3:46650885-46650896

No.	Distal block	Cell Line	Cell type
1	chr3:46650273..46651172-chr3:46707945..46708857,6	MCF-7	breast:
2	chr3:46650761..46651345-chr3:46671138..46672058,2	MCF-7	breast:
3	chr3:46650273..46651172-chr3:46707945..46708857,7	MCF-7	breast:

Variant related genes	Relation type
TDGF1	TF binding region

Extended variants
information (count: 23 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs13070740	1.00[MKK][hapmap]
rs13093282	1.00[MKK][hapmap]
rs1520492	0.96[ASN][1000 genomes]
rs1520494	0.96[ASN][1000 genomes]
rs17078977	0.96[ASN][1000 genomes]
rs2280413	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs2280414	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs4312690	1.00[ASW][hapmap];1.00[MKK][hapmap]
rs55740502	0.96[ASN][1000 genomes]
rs57417282	0.96[ASN][1000 genomes]
rs58599738	0.96[ASN][1000 genomes]
rs58647844	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73075520	0.82[AMR][1000 genomes];0.94[ASN][1000 genomes]
rs73075538	0.95[ASN][1000 genomes]
rs73075539	0.95[ASN][1000 genomes]
rs73075540	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73075542	0.99[ASN][1000 genomes]
rs73075543	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73075555	0.96[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73075561	1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs73075569	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1013306	chr3:46469014-46698538	Weak transcription Enhancers Strong transcription Active TSS Bivalent Enhancer Flanking Active TSS Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases
2	nsv876738	chr3:46639048-46680063	Enhancers Flanking Active TSS Active TSS Weak transcription Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Plasma amyloid beta peptide concentrations (ABx-42)	24535457	GWAS catalog

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:46628800-46651000	Weak transcription	Right Atrium	heart
2	chr3:46646200-46654000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:46646600-46651000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr3:46648200-46652000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
5	chr3:46648200-46652000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr3:46648600-46652000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
7	chr3:46649600-46651000	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr3:46649600-46651000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
9	chr3:46649800-46651200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr3:46650000-46651000	Weak transcription	HUES48 Cell Line	embryonic stem cell
11	chr3:46650000-46651400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
12	chr3:46650400-46651800	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr3:46650600-46651000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr3:46650600-46651200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
15	chr3:46650600-46651200	Enhancers	Adipose Nuclei	Adipose
16	chr3:46650600-46651400	Bivalent Enhancer	Fetal Kidney	kidney
17	chr3:46650600-46651400	Bivalent Enhancer	Fetal Muscle Leg	muscle
18	chr3:46650600-46651400	Enhancers	Skeletal Muscle Male	skeletal muscle
19	chr3:46650600-46651600	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
20	chr3:46650600-46651600	Enhancers	Placenta	Placenta
21	chr3:46650600-46652000	Enhancers	ES-I3 Cell Line	embryonic stem cell
22	chr3:46650600-46652000	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr3:46650800-46651000	Bivalent Enhancer	Osteobl	bone
24	chr3:46650800-46651200	Bivalent Enhancer	Muscle Satellite Cultured Cells	--
25	chr3:46650800-46651200	Flanking Active TSS	Hela-S3	cervix
26	chr3:46650800-46651400	Enhancers	HUES64 Cell Line	embryonic stem cell
27	chr3:46650800-46651400	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
28	chr3:46650800-46651400	Enhancers	Liver	Liver
29	chr3:46650800-46651400	Bivalent Enhancer	HepG2	liver
30	chr3:46650800-46651600	Enhancers	Skeletal Muscle Female	skeletal muscle
31	chr3:46650800-46651800	Bivalent Enhancer	NHEK	skin
32	chr3:46650800-46652000	Enhancers	H9 Cell Line	embryonic stem cell
33	chr3:46650800-46652000	Enhancers	iPS-15b Cell Line	embryonic stem cell
34	chr3:46650800-46654600	Enhancers	Breast Myoepithelial Primary Cells	Breast

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