Variant report

Variant	rs6479408
Chromosome Location	chr9:94903215-94903216
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	MXI1	chr9:94902467-94903909	SK-N-SH	brain:	n/a	n/a
2	MXI1	chr9:94902085-94904234	IMR90	lung:	n/a	n/a
3	CTCF	chr9:94903080-94903230	HUVEC	blood vessel:	n/a	n/a
4	CTCF	chr9:94903180-94903330	HPF	lung:	n/a	n/a
5	CTCF	chr9:94903120-94903270	GM12872	blood:	n/a	n/a
6	CTCF	chr9:94903080-94903230	GM12866	blood:	n/a	n/a
7	SIN3A	chr9:94902559-94903727	H1-hESC	embryonic stem cell:	n/a	chr9:94902732-94902741
8	SMC3	chr9:94902439-94903811	SK-N-SH	brain:	n/a	chr9:94902741-94902755 chr9:94902745-94902755
9	CTCF	chr9:94902024-94903401	A549	lung:	n/a	chr9:94902742-94902755 chr9:94902741-94902762 chr9:94902739-94902757 chr9:94902740-94902756 chr9:94902739-94902752

No.	Distal block	Cell Line	Cell type
1	chr9:94900325..94903739-chr9:94909399..94912070,4	MCF-7	breast:
2	chr1:117477349..117478025-chr9:94902653..94903339,2	MCF-7	breast:
3	chr9:94901685..94904988-chr9:95003695..95006795,3	MCF-7	breast:
4	chr9:94898906..94903668-chr9:95086648..95090271,5	MCF-7	breast:
5	chr9:94902503..94903236-chr9:95396725..95397397,2	MCF-7	breast:
6	chr9:94902223..94905302-chr9:94908199..94910430,4	MCF-7	breast:
7	chr9:94902180..94903465-chr9:95004247..95005390,7	MCF-7	breast:

Variant related genes	Relation type
LINC00475	TF binding region
ENSG00000196305	Chromatin interaction
ENSG00000225511	Chromatin interaction
ENSG00000188312	Chromatin interaction
ENSG00000198000	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:10)

rs_ID	r²[population]
rs10739926	0.86[ASN][1000 genomes]
rs10992251	0.81[EUR][1000 genomes]
rs1105085	0.98[ASN][1000 genomes]
rs11788534	0.80[ASN][1000 genomes]
rs11794148	0.88[ASN][1000 genomes]
rs1964170	0.98[ASN][1000 genomes]
rs2274921	0.84[AMR][1000 genomes]
rs3858095	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3927571	0.82[EUR][1000 genomes]
rs7024547	0.86[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	nsv949008	chr9:94500776-95182133	Enhancers ZNF genes & repeats Weak transcription Bivalent Enhancer Strong transcription Flanking Active TSS Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
2	nsv1050845	chr9:94687959-95312406	Weak transcription Enhancers Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	58 gene(s)	inside rSNPs	diseases
3	nsv1046733	chr9:94690622-95138564	Genic enhancers Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
4	nsv530947	chr9:94697309-95093377	Weak transcription Bivalent Enhancer Strong transcription Enhancers Active TSS Bivalent/Poised TSS Flanking Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	49 gene(s)	inside rSNPs	diseases
5	nsv917089	chr9:94857047-95099848	Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv969760	chr9:94877924-94966209	Flanking Bivalent TSS/Enh Weak transcription Flanking Active TSS Enhancers Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
7	nsv893572	chr9:94891778-94944778	Enhancers Bivalent Enhancer Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
8	nsv972778	chr9:94902068-94908273	Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr9:94902200-94904200	Enhancers	Liver	Liver
2	chr9:94902600-94903400	Flanking Active TSS	IMR90 fetal lung fibroblasts Cell Line	lung
3	chr9:94902600-94903600	Bivalent Enhancer	Primary Natural Killer cells fromperipheralblood	blood
4	chr9:94902600-94903600	Bivalent Enhancer	Fetal Thymus	thymus
5	chr9:94902600-94903600	Flanking Bivalent TSS/Enh	Stomach Smooth Muscle	stomach
6	chr9:94902800-94903400	Bivalent Enhancer	H9 Derived Neuron Cultured Cells	ES cell derived
7	chr9:94902800-94903400	Bivalent Enhancer	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	HUES6 Cell Line	embryonic stem cell
9	chr9:94902800-94903400	Bivalent Enhancer	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr9:94902800-94903400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
11	chr9:94902800-94903400	Flanking Active TSS	Breast Myoepithelial Primary Cells	Breast
12	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
13	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Primary T helper naive cells fromperipheralblood	blood
14	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Primary T helper cells PMA-I stimulated	--
15	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Primary T helper 17 cells PMA-I stimulated	--
16	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Primary T helper cells fromperipheralblood	blood
17	chr9:94902800-94903400	Flanking Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr9:94902800-94903400	Flanking Active TSS	Muscle Satellite Cultured Cells	--
19	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Foreskin Keratinocyte Primary Cells skin02	Skin
21	chr9:94902800-94903400	Flanking Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
22	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
23	chr9:94902800-94903400	Flanking Active TSS	Brain Anterior Caudate	brain
24	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Duodenum Mucosa	Duodenum
25	chr9:94902800-94903400	Enhancers	Esophagus	oesophagus
26	chr9:94902800-94903400	Flanking Active TSS	Ovary	ovary
27	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 29	rectum
28	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Rectal Mucosa Donor 31	rectum
29	chr9:94902800-94903400	Bivalent Enhancer	Sigmoid Colon	Sigmoid Colon
30	chr9:94902800-94903400	Flanking Bivalent TSS/Enh	Skeletal Muscle Male	skeletal muscle
31	chr9:94902800-94903400	Flanking Active TSS	A549	lung
32	chr9:94902800-94903400	Flanking Active TSS	HSMM	muscle
33	chr9:94902800-94903400	Flanking Active TSS	HUVEC	blood vessel
34	chr9:94902800-94903400	Enhancers	K562	blood
35	chr9:94902800-94903400	Flanking Active TSS	NH-A	brain
36	chr9:94902800-94903400	Flanking Active TSS	NHDF-Ad	bronchial
37	chr9:94902800-94903400	Flanking Active TSS	Osteobl	bone
38	chr9:94902800-94903600	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
39	chr9:94902800-94903600	Flanking Bivalent TSS/Enh	Fetal Muscle Trunk	muscle
40	chr9:94902800-94903800	Bivalent Enhancer	Primary mononuclear cells fromperipheralblood	Blood
41	chr9:94902800-94903800	Flanking Bivalent TSS/Enh	Brain Hippocampus Middle	brain
42	chr9:94902800-94904000	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
43	chr9:94902800-94904000	Enhancers	Primary hematopoietic stem cells	blood
44	chr9:94902800-94904000	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
45	chr9:94902800-94904000	Bivalent Enhancer	Primary T helper memory cells from peripheral blood 1	blood
46	chr9:94902800-94904000	Bivalent Enhancer	Monocytes-CD14+_RO01746	blood
47	chr9:94902800-94904200	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr9:94902800-94904200	Active TSS	Fetal Kidney	kidney
49	chr9:94902800-94904200	Enhancers	Lung	lung
50	chr9:94903000-94903400	Flanking Bivalent TSS/Enh	ES-I3 Cell Line	embryonic stem cell

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