Variant report

Variant	rs9489217
Chromosome Location	chr6:117869850-117869851
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr6:117802435..117804149-chr6:117867844..117870833,3	MCF-7	breast:
2	chr6:117868602..117871781-chr6:117879048..117881527,3	K562	blood:

Variant related genes	Relation type
ENSG00000164465	Chromatin interaction

Extended variants
information (count: 15 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs2071825	0.82[CEU][hapmap]
rs210618	0.81[ASN][1000 genomes]
rs210619	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210620	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210621	0.81[ASN][1000 genomes]
rs210625	0.93[ASW][hapmap];0.92[CEU][hapmap];1.00[CHB][hapmap];0.98[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.91[MEX][hapmap];0.80[MKK][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs210627	0.80[ASN][1000 genomes]
rs210628	0.80[ASN][1000 genomes]
rs2134086	0.82[AMR][1000 genomes]
rs2134087	0.82[ASN][1000 genomes]
rs389663	0.95[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap];0.91[ASN][1000 genomes]
rs8088	1.00[ASW][hapmap];0.92[CEU][hapmap];0.95[CHB][hapmap];1.00[CHD][hapmap];0.97[GIH][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];0.86[MEX][hapmap];0.94[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320608	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9320609	0.93[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv532050	chr6:117528154-118203005	ZNF genes & repeats Enhancers Bivalent Enhancer Active TSS Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:119 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:117858200-117870400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr6:117863400-117872200	Genic enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr6:117864000-117870200	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr6:117865600-117870600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr6:117866600-117870400	Weak transcription	K562	blood
6	chr6:117868200-117872000	Genic enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr6:117868600-117870200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
8	chr6:117868600-117870400	Enhancers	Primary hematopoietic stem cells	blood
9	chr6:117868600-117870400	Transcr. at gene 5' and 3'	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
10	chr6:117868600-117870600	Flanking Active TSS	Primary T helper cells fromperipheralblood	blood
11	chr6:117868600-117871000	Flanking Active TSS	Primary T regulatory cells fromperipheralblood	blood
12	chr6:117868600-117872400	Genic enhancers	NHEK	skin
13	chr6:117868800-117870000	Flanking Active TSS	Primary hematopoietic stem cells short term culture	blood
14	chr6:117868800-117870000	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
15	chr6:117868800-117870000	Flanking Active TSS	Primary Natural Killer cells fromperipheralblood	blood
16	chr6:117868800-117870000	Active TSS	Brain Inferior Temporal Lobe	brain
17	chr6:117868800-117870000	Enhancers	Fetal Brain Male	brain
18	chr6:117868800-117870000	Active TSS	Fetal Brain Female	brain
19	chr6:117868800-117870000	Flanking Active TSS	Fetal Muscle Leg	muscle
20	chr6:117868800-117870200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr6:117868800-117870200	Active TSS	Colon Smooth Muscle	Colon
22	chr6:117868800-117870200	Genic enhancers	NHLF	lung
23	chr6:117868800-117870400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
24	chr6:117868800-117871200	Flanking Active TSS	Primary T helper cells PMA-I stimulated	--
25	chr6:117869000-117870200	Active TSS	Primary T killer memory cells from peripheral blood	blood
26	chr6:117869000-117870400	Active TSS	Primary T helper memory cells from peripheral blood 1	blood
27	chr6:117869000-117870400	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr6:117869000-117871000	Genic enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr6:117869200-117870200	Transcr. at gene 5' and 3'	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr6:117869200-117870400	Active TSS	Pancreatic Islets	Pancreatic Islet
31	chr6:117869200-117870400	Active TSS	Rectal Mucosa Donor 29	rectum
32	chr6:117869400-117870000	Flanking Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
33	chr6:117869400-117870000	Flanking Active TSS	Brain Cingulate Gyrus	brain
34	chr6:117869400-117870000	Flanking Active TSS	HSMM	muscle
35	chr6:117869400-117870000	Flanking Active TSS	NH-A	brain
36	chr6:117869400-117870400	Genic enhancers	HepG2	liver
37	chr6:117869400-117870600	Flanking Active TSS	Primary T cells from cord blood	blood
38	chr6:117869400-117870800	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
39	chr6:117869400-117871000	Strong transcription	Sigmoid Colon	Sigmoid Colon
40	chr6:117869400-117872200	Enhancers	ES-WA7 Cell Line	embryonic stem cell
41	chr6:117869600-117870000	Flanking Active TSS	Brain Hippocampus Middle	brain
42	chr6:117869600-117870000	Enhancers	Stomach Mucosa	stomach
43	chr6:117869600-117870400	Flanking Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
44	chr6:117869600-117870400	Enhancers	Primary B cells from cord blood	blood
45	chr6:117869600-117870400	Active TSS	Primary T cells effector/memory enriched fromperipheralblood	blood
46	chr6:117869600-117870400	Flanking Active TSS	Fetal Heart	heart
47	chr6:117869600-117870400	Enhancers	Placenta	Placenta
48	chr6:117869600-117870600	Genic enhancers	GM12878-XiMat	blood
49	chr6:117869600-117870600	Enhancers	Hela-S3	cervix
50	chr6:117869600-117870600	Genic enhancers	HMEC	breast

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