Variant report

Variant	rs9462089
Chromosome Location	chr6:35440192-35440193
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:12)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:12 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35419539..35422466-chr6:35438622..35441201,2	MCF-7	breast:
2	chr6:35308405..35313609-chr6:35434054..35440248,12	K562	blood:
3	chr6:35260730..35269335-chr6:35433870..35444063,22	MCF-7	breast:
4	chr6:35439431..35441944-chr6:35514105..35515809,2	MCF-7	breast:
5	chr6:34855012..34857706-chr6:35439767..35441734,2	K562	blood:
6	chr18:45406363..45407026-chr6:35439781..35440543,2	Hela-S3	cervix:
7	chr6:35237573..35240091-chr6:35439792..35442859,3	K562	blood:
8	chr1:109234339..109236441-chr6:35439456..35441815,2	MCF-7	breast:
9	chr6:35438538..35440763-chr6:35753826..35756739,2	K562	blood:
10	chr6:35263451..35267137-chr6:35438747..35441852,5	K562	blood:
11	chr6:35438691..35440741-chr6:35704071..35706760,2	K562	blood:
12	chr6:35415818..35424678-chr6:35432486..35440672,36	K562	blood:

No data

Variant related genes	Relation type
ENSG00000023892	Chromatin interaction
ENSG00000232909	Chromatin interaction
ENSG00000157343	Chromatin interaction
ENSG00000134186	Chromatin interaction
ENSG00000204140	Chromatin interaction
ENSG00000065029	Chromatin interaction
ENSG00000064995	Chromatin interaction
ENSG00000112039	Chromatin interaction
ENSG00000064999	Chromatin interaction
ENSG00000112033	Chromatin interaction

Extended variants
information (count: 32 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:25)

rs_ID	r²[population]
rs11553979	0.95[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11962317	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs16876584	0.97[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16876587	0.98[ASN][1000 genomes]
rs3800376	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.94[AFR][1000 genomes];0.81[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs41271261	0.96[AFR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs45479891	0.98[ASN][1000 genomes]
rs6457822	1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6457823	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs6457824	1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[ASN][1000 genomes]
rs6914178	0.98[ASN][1000 genomes]
rs6926662	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs6927202	0.98[ASN][1000 genomes]
rs6927367	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs7739161	0.89[AFR][1000 genomes]
rs7746718	0.98[ASN][1000 genomes]
rs7767821	0.84[ASN][1000 genomes]
rs7768070	0.98[ASN][1000 genomes]
rs9462087	0.93[ASN][1000 genomes]
rs9462088	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9470027	0.87[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470030	0.93[AFR][1000 genomes];0.81[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs9470033	1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[ASN][1000 genomes]
rs9470035	0.98[ASN][1000 genomes]
rs9470038	0.97[AFR][1000 genomes];0.84[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv830641	chr6:35282534-35440603	Enhancers Weak transcription Flanking Active TSS Genic enhancers Strong transcription Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
2	nsv528351	chr6:35377922-35465786	Flanking Active TSS Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Enhancers Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	69 gene(s)	inside rSNPs	diseases
3	nsv885799	chr6:35378778-35442397	Active TSS Strong transcription Weak transcription Flanking Active TSS Genic enhancers Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
4	nsv462908	chr6:35378778-35457396	Enhancers Weak transcription Bivalent/Poised TSS Genic enhancers Strong transcription Flanking Active TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
5	nsv602910	chr6:35378778-35457396	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent/Poised TSS Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	55 gene(s)	inside rSNPs	diseases
6	nsv519370	chr6:35378778-35537406	Weak transcription Bivalent Enhancer Enhancers Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	72 gene(s)	inside rSNPs	diseases
7	nsv984463	chr6:35432948-35477634	Weak transcription Enhancers Strong transcription Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region miRNA	67 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35435200-35440200	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin02	Skin
2	chr6:35436200-35440400	Transcr. at gene 5' and 3'	Primary T helper 17 cells PMA-I stimulated	--
3	chr6:35436200-35440600	Transcr. at gene 5' and 3'	Foreskin Fibroblast Primary Cells skin01	Skin
4	chr6:35436400-35440200	Transcr. at gene 5' and 3'	Foreskin Keratinocyte Primary Cells skin03	Skin
5	chr6:35436400-35440200	Transcr. at gene 5' and 3'	NHEK	skin
6	chr6:35436400-35440600	Transcr. at gene 5' and 3'	Primary T helper cells PMA-I stimulated	--
7	chr6:35437000-35440800	Transcr. at gene 5' and 3'	Breast Myoepithelial Primary Cells	Breast
8	chr6:35437200-35440400	Transcr. at gene 5' and 3'	HUES64 Cell Line	embryonic stem cell
9	chr6:35437200-35440400	Transcr. at gene 5' and 3'	K562	blood
10	chr6:35437200-35440600	Transcr. at gene 5' and 3'	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr6:35437600-35449200	Strong transcription	Aorta	Aorta
12	chr6:35437800-35440400	Genic enhancers	Sigmoid Colon	Sigmoid Colon
13	chr6:35437800-35443800	Genic enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr6:35437800-35446200	Weak transcription	Pancreatic Islets	Pancreatic Islet
15	chr6:35437800-35451000	Weak transcription	Primary neutrophils fromperipheralblood	blood
16	chr6:35438000-35440200	Genic enhancers	Primary T cells fromperipheralblood	blood
17	chr6:35438000-35440200	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
18	chr6:35438000-35440200	Genic enhancers	Cortex derived primary cultured neurospheres	brain
19	chr6:35438000-35440400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
20	chr6:35438000-35440400	Genic enhancers	Fetal Stomach	stomach
21	chr6:35438000-35440600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
22	chr6:35438000-35440600	Genic enhancers	Liver	Liver
23	chr6:35438000-35441400	Genic enhancers	Placenta	Placenta
24	chr6:35438000-35443200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
25	chr6:35438000-35455800	Weak transcription	Brain Angular Gyrus	brain
26	chr6:35438200-35440200	Genic enhancers	Fetal Intestine Large	intestine
27	chr6:35438200-35441200	Strong transcription	Brain Hippocampus Middle	brain
28	chr6:35438200-35441400	Genic enhancers	Left Ventricle	heart
29	chr6:35438200-35442400	Genic enhancers	Fetal Muscle Leg	muscle
30	chr6:35438200-35442600	Genic enhancers	Fetal Muscle Trunk	muscle
31	chr6:35438200-35444200	Strong transcription	Thymus	Thymus
32	chr6:35438200-35458000	Weak transcription	Brain Inferior Temporal Lobe	brain
33	chr6:35438400-35440200	Genic enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr6:35438400-35440200	Genic enhancers	ES-UCSF4 Cell Line	embryonic stem cell
35	chr6:35438400-35440200	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
36	chr6:35438400-35440200	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
37	chr6:35438400-35440400	Genic enhancers	Adipose Nuclei	Adipose
38	chr6:35438400-35440400	Genic enhancers	Rectal Smooth Muscle	rectum
39	chr6:35438400-35441000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
40	chr6:35438400-35441200	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
41	chr6:35438400-35441200	Genic enhancers	Duodenum Smooth Muscle	Duodenum
42	chr6:35438400-35441200	Genic enhancers	Pancreas	Pancrea
43	chr6:35438400-35441800	Genic enhancers	Fetal Adrenal Gland	Adrenal Gland
44	chr6:35438400-35442400	Strong transcription	Monocytes-CD14+_RO01746	blood
45	chr6:35438400-35442800	Weak transcription	Primary hematopoietic stem cells	blood
46	chr6:35438400-35443600	Strong transcription	Esophagus	oesophagus
47	chr6:35438400-35449600	Strong transcription	Gastric	stomach
48	chr6:35438600-35440200	Genic enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
49	chr6:35438800-35440400	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
50	chr6:35438800-35440600	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links