Variant report

Variant	rs9289977
Chromosome Location	chr3:156842653-156842654
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:156839274..156841374-chr3:156841573..156843251,2	MCF-7	breast:
2	chr3:156806562..156808405-chr3:156841646..156844767,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000241135	Chromatin interaction
ENSG00000243629	Chromatin interaction

Extended variants
information (count: 8 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs13064954	0.86[CHB][hapmap]
rs35196422	0.85[ASN][1000 genomes]
rs9289976	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[LWK][hapmap];1.00[MEX][hapmap];0.92[MKK][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9816148	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9832544	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9870220	1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[AMR][1000 genomes];0.98[EUR][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	esv3349885	chr3:156685409-156878910	Flanking Active TSS Weak transcription Enhancers Transcr. at gene 5' and 3' Strong transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
2	nsv829766	chr3:156811536-157020551	Enhancers Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	144 gene(s)	inside rSNPs	diseases

No data

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:156819600-156846400	Weak transcription	Fetal Kidney	kidney
2	chr3:156833600-156846600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
3	chr3:156834200-156842800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr3:156834200-156842800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
5	chr3:156834200-156844400	Weak transcription	Right Ventricle	heart
6	chr3:156834200-156845400	Weak transcription	Right Atrium	heart
7	chr3:156836800-156847200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr3:156837000-156850400	Enhancers	Fetal Intestine Small	intestine
9	chr3:156837200-156846600	Enhancers	Fetal Heart	heart
10	chr3:156837400-156845200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr3:156838000-156843800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:156838200-156843000	Weak transcription	K562	blood
13	chr3:156838200-156844800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
14	chr3:156838400-156846000	Weak transcription	Lung	lung
15	chr3:156838400-156846800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr3:156838400-156851400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr3:156838600-156845400	Weak transcription	Colonic Mucosa	Colon
18	chr3:156838600-156845400	Enhancers	NHEK	skin
19	chr3:156838800-156846000	Enhancers	HepG2	liver
20	chr3:156839200-156848200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
21	chr3:156840200-156843800	Weak transcription	Rectal Mucosa Donor 29	rectum
22	chr3:156840200-156844600	Weak transcription	Fetal Thymus	thymus
23	chr3:156840200-156845400	Weak transcription	NHDF-Ad	bronchial
24	chr3:156840400-156843000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr3:156840400-156843000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
26	chr3:156840400-156845800	Weak transcription	HUVEC	blood vessel
27	chr3:156840400-156847800	Enhancers	HMEC	breast
28	chr3:156840600-156842800	Weak transcription	Hela-S3	cervix
29	chr3:156840600-156843000	Weak transcription	Osteobl	bone
30	chr3:156840600-156845200	Weak transcription	HSMMtube	muscle
31	chr3:156840600-156846400	Weak transcription	Psoas Muscle	Psoas
32	chr3:156840600-156847800	Weak transcription	Small Intestine	intestine
33	chr3:156840800-156844000	Weak transcription	Sigmoid Colon	Sigmoid Colon
34	chr3:156841000-156846200	Weak transcription	Brain Substantia Nigra	brain
35	chr3:156841000-156846800	Weak transcription	Fetal Lung	lung
36	chr3:156841200-156842800	Weak transcription	HSMM	muscle
37	chr3:156841200-156846400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr3:156841200-156846800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr3:156841200-156848000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
40	chr3:156841400-156842800	Weak transcription	A549	lung
41	chr3:156841400-156842800	Weak transcription	NH-A	brain
42	chr3:156841400-156845200	Weak transcription	NHLF	lung
43	chr3:156841600-156845000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
44	chr3:156841800-156842800	Weak transcription	Left Ventricle	heart
45	chr3:156841800-156842800	Weak transcription	Stomach Mucosa	stomach
46	chr3:156842200-156843200	Enhancers	Brain Inferior Temporal Lobe	brain
47	chr3:156842200-156845200	Weak transcription	Liver	Liver
48	chr3:156842400-156843000	Enhancers	Placenta Amnion	Placenta Amnion
49	chr3:156842400-156844800	Enhancers	Rectal Mucosa Donor 31	rectum
50	chr3:156842400-156845800	Enhancers	Muscle Satellite Cultured Cells	--

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