Variant report

Variant	rs9469962
Chromosome Location	chr6:35188408-35188409
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:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr6:35186126..35189088-chr6:35223923..35225540,2	K562	blood:
2	chr6:35177824..35181731-chr6:35185438..35190079,5	K562	blood:
3	chr6:35188260..35190147-chr6:35205667..35207207,2	K562	blood:
4	chr6:35086962..35089707-chr6:35186817..35189390,2	K562	blood:
5	chr6:35182167..35187066-chr6:35187567..35191599,8	K562	blood:
6	chr6:35172567..35174119-chr6:35186872..35189196,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-TCP11-2	chr6:35188147-35189134	NONHSAT112168
2	lnc-TCP11-2	chr6:35188147-35192407	ENSG00000272374.1

No data

Variant related genes	Relation type
ENSG00000124678	Chromatin interaction
ENSG00000146197	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs57127611	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs60812576	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs61534122	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9296145	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462061	0.99[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9462070	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469952	0.85[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469965	0.82[AFR][1000 genomes]
rs9469966	0.82[AFR][1000 genomes]
rs9469969	0.82[AFR][1000 genomes]
rs9469973	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469974	0.92[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469983	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9469987	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470003	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]
rs9470005	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3428128	chr6:35150524-35225843	Bivalent Enhancer Enhancers Genic enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Strong transcription Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv2758047	chr6:35168116-35291002	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Active TSS Weak transcription Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases
3	esv2759419	chr6:35168116-35291002	Weak transcription Flanking Active TSS Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	26 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:43 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:35182400-35209000	Weak transcription	A549	lung
2	chr6:35182600-35198600	Weak transcription	Gastric	stomach
3	chr6:35183200-35198800	Weak transcription	Ovary	ovary
4	chr6:35183600-35189000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
5	chr6:35184800-35205600	Weak transcription	Fetal Brain Female	brain
6	chr6:35185400-35198800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
7	chr6:35185600-35189200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr6:35185600-35194200	Enhancers	Fetal Heart	heart
9	chr6:35185800-35198400	Weak transcription	Brain Cingulate Gyrus	brain
10	chr6:35186200-35202800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr6:35186400-35188600	Enhancers	Right Ventricle	heart
12	chr6:35186400-35198000	Weak transcription	Rectal Smooth Muscle	rectum
13	chr6:35186400-35212000	Weak transcription	NHDF-Ad	bronchial
14	chr6:35186600-35189600	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr6:35186600-35193200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:35186600-35198200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
17	chr6:35186600-35204600	Weak transcription	Placenta Amnion	Placenta Amnion
18	chr6:35186600-35205400	Weak transcription	Fetal Muscle Trunk	muscle
19	chr6:35186800-35212000	Weak transcription	Dnd41	blood
20	chr6:35187000-35196400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr6:35187000-35197600	Weak transcription	Stomach Smooth Muscle	stomach
22	chr6:35187200-35188600	Enhancers	Aorta	Aorta
23	chr6:35187200-35189800	Genic enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
24	chr6:35187400-35198400	Weak transcription	Brain Hippocampus Middle	brain
25	chr6:35187600-35198400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr6:35187800-35192600	Weak transcription	Brain Anterior Caudate	brain
27	chr6:35188000-35188600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr6:35188000-35188800	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr6:35188000-35188800	Weak transcription	Left Ventricle	heart
30	chr6:35188000-35190200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
31	chr6:35188000-35191400	Weak transcription	Fetal Stomach	stomach
32	chr6:35188000-35195200	Weak transcription	Lung	lung
33	chr6:35188000-35198400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr6:35188000-35198600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
35	chr6:35188000-35199400	Weak transcription	Muscle Satellite Cultured Cells	--
36	chr6:35188200-35190000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr6:35188200-35200400	Genic enhancers	Osteobl	bone
38	chr6:35188200-35205800	Weak transcription	Fetal Kidney	kidney
39	chr6:35188200-35206400	Weak transcription	NH-A	brain
40	chr6:35188400-35188800	Enhancers	HSMM	muscle
41	chr6:35188400-35189000	Enhancers	HSMMtube	muscle
42	chr6:35188400-35197200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr6:35188400-35199600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived

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