Variant report

Variant	rs9446984
Chromosome Location	chr6:74409895-74409896
allele	A/C
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	FOS	chr6:74409771-74410007	MCF10A-Er-Src	breast:	n/a	n/a
2	POLR2A	chr6:74409251-74409900	HUVEC	blood vessel:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:74404503..74407805-chr6:74409616..74412455,3	MCF-7	breast:
2	chr6:74230105..74232138-chr6:74409419..74412295,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231652	TF binding region
ENSG00000231652	Chromatin interaction
ENSG00000156535	Chromatin interaction
ENSG00000156508	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 2 )

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

rs_ID	r²[population]
rs3764240	0.82[CEU][hapmap]
rs55982851	0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs56171536	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs56311419	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs72953369	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs72953372	0.85[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs72953375	0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9442945	0.85[LWK][hapmap]
rs9442946	1.00[CEU][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs9442947	1.00[ASW][hapmap];1.00[GIH][hapmap];0.86[JPT][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9442948	0.82[AFR][1000 genomes]
rs9446983	0.90[LWK][hapmap]
rs9446986	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9446988	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.86[AFR][1000 genomes];0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][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	esv3410973	chr6:73716033-74419545	Active TSS Bivalent Enhancer Flanking Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	191 gene(s)	inside rSNPs	diseases
2	nsv886158	chr6:74126084-74436825	Weak transcription Active TSS Strong transcription Enhancers Genic enhancers Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	179 gene(s)	inside rSNPs	diseases
3	nsv1027968	chr6:74155378-74521923	Active TSS Flanking Active TSS Strong transcription Bivalent Enhancer Weak transcription Enhancers Genic enhancers 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 target site	178 gene(s)	inside rSNPs	diseases
4	nsv538305	chr6:74155378-74521923	Flanking Active TSS Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	178 gene(s)	inside rSNPs	diseases
5	nsv1023250	chr6:74189642-74605976	Strong transcription Weak transcription Genic enhancers Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
6	nsv538306	chr6:74189642-74605976	Strong transcription Enhancers Active TSS Bivalent Enhancer Weak transcription Flanking Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	172 gene(s)	inside rSNPs	diseases
7	nsv1029927	chr6:74300496-74424355	Weak transcription Strong transcription Enhancers Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
8	nsv1027691	chr6:74302980-74417450	Weak transcription Enhancers Strong transcription Active TSS Genic enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs9446984	CD109	cis	lymphoblastoid	seeQTL
rs9446984	CD109	cis	multi-tissue	Pritchard

Chromatin state (count:57 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:74406600-74412800	Active TSS	Primary T helper cells PMA-I stimulated	--
2	chr6:74406600-74414000	Weak transcription	Placenta	Placenta
3	chr6:74407000-74410000	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:74407200-74413000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:74407200-74413600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr6:74407200-74414200	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr6:74407200-74414200	Weak transcription	Stomach Smooth Muscle	stomach
8	chr6:74407200-74421800	Weak transcription	Duodenum Smooth Muscle	Duodenum
9	chr6:74407200-74422400	Weak transcription	Fetal Lung	lung
10	chr6:74407200-74423800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr6:74407200-74424800	Weak transcription	Fetal Muscle Trunk	muscle
12	chr6:74407400-74413000	Weak transcription	NH-A	brain
13	chr6:74407400-74414000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:74407400-74414400	Weak transcription	Brain Anterior Caudate	brain
15	chr6:74407400-74423000	Weak transcription	Fetal Muscle Leg	muscle
16	chr6:74407600-74412000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
17	chr6:74407600-74412800	Weak transcription	NHLF	lung
18	chr6:74407600-74413000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
19	chr6:74407600-74413000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
20	chr6:74407600-74413000	Weak transcription	Placenta Amnion	Placenta Amnion
21	chr6:74407600-74413200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
22	chr6:74407600-74413600	Weak transcription	Rectal Smooth Muscle	rectum
23	chr6:74407600-74414000	Weak transcription	HUES6 Cell Line	embryonic stem cell
24	chr6:74407600-74414000	Weak transcription	Primary monocytes fromperipheralblood	blood
25	chr6:74407600-74414000	Weak transcription	Fetal Thymus	thymus
26	chr6:74407600-74414000	Weak transcription	Left Ventricle	heart
27	chr6:74407600-74414000	Weak transcription	Monocytes-CD14+_RO01746	blood
28	chr6:74407600-74424000	Weak transcription	Right Ventricle	heart
29	chr6:74407800-74410400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr6:74407800-74412600	Weak transcription	Hela-S3	cervix
31	chr6:74407800-74412800	Weak transcription	Fetal Heart	heart
32	chr6:74407800-74413400	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr6:74407800-74415800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
34	chr6:74407800-74416800	Weak transcription	Thymus	Thymus
35	chr6:74408000-74412400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
36	chr6:74408000-74412600	Weak transcription	Primary T cells from cord blood	blood
37	chr6:74408000-74412800	Weak transcription	Muscle Satellite Cultured Cells	--
38	chr6:74408000-74446800	Weak transcription	Dnd41	blood
39	chr6:74408600-74410000	Genic enhancers	HMEC	breast
40	chr6:74408600-74410000	Flanking Active TSS	HUVEC	blood vessel
41	chr6:74408600-74410400	Enhancers	Primary hematopoietic stem cells short term culture	blood
42	chr6:74408600-74410400	Active TSS	Primary T helper 17 cells PMA-I stimulated	--
43	chr6:74408600-74414400	Genic enhancers	NHDF-Ad	bronchial
44	chr6:74408800-74411200	Weak transcription	Osteobl	bone
45	chr6:74408800-74414600	Weak transcription	HSMM	muscle
46	chr6:74409000-74411200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr6:74409200-74410200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
48	chr6:74409200-74410200	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
49	chr6:74409400-74410200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
50	chr6:74409600-74410200	Enhancers	Primary hematopoietic stem cells	blood

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links