Variant report

Variant	rs12662020
Chromosome Location	chr6:163767147-163767148
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr6:163766963..163769650-chr6:163833960..163836613,2	MCF-7	breast:
2	chr6:163765676..163767710-chr6:163771048..163773547,3	K562	blood:
3	chr6:163757980..163760301-chr6:163766336..163768728,2	K562	blood:

Variant related genes	Relation type
ENSG00000270419	Chromatin interaction
ENSG00000112531	Chromatin interaction

Extended variants
information (count: 9 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs12662070	1.00[CHB][hapmap];0.91[JPT][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs12664178	0.89[ASN][1000 genomes]
rs12665052	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.91[JPT][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12665288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73603780	1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv932127	chr6:163000261-163950870	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Strong transcription Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
2	nsv1022610	chr6:163591786-163814041	Weak transcription Enhancers Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
3	nsv605188	chr6:163697439-163772096	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
4	nsv534621	chr6:163731741-163950870	Bivalent/Poised TSS Enhancers Flanking Active TSS Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:42 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr6:163745600-163773600	Enhancers	Brain Substantia Nigra	brain
2	chr6:163759000-163768400	Enhancers	Cortex derived primary cultured neurospheres	brain
3	chr6:163760800-163767200	Enhancers	Brain Hippocampus Middle	brain
4	chr6:163760800-163767400	Weak transcription	NH-A	brain
5	chr6:163761400-163767200	Enhancers	Brain Anterior Caudate	brain
6	chr6:163763200-163768000	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr6:163763400-163767200	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr6:163763800-163767400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
9	chr6:163763800-163768000	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr6:163764000-163767400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
11	chr6:163764000-163768600	Enhancers	Right Ventricle	heart
12	chr6:163764200-163767400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
13	chr6:163764400-163769400	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr6:163764600-163767600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
15	chr6:163764800-163767200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr6:163764800-163767200	Enhancers	Brain Cingulate Gyrus	brain
17	chr6:163765000-163767200	Weak transcription	Fetal Heart	heart
18	chr6:163765000-163774000	Weak transcription	Spleen	Spleen
19	chr6:163765200-163767600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
20	chr6:163765600-163767200	Enhancers	Fetal Muscle Leg	muscle
21	chr6:163765600-163767400	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
22	chr6:163765600-163773000	Enhancers	Brain Angular Gyrus	brain
23	chr6:163766000-163767800	Weak transcription	Primary monocytes fromperipheralblood	blood
24	chr6:163766000-163771400	Weak transcription	Monocytes-CD14+_RO01746	blood
25	chr6:163766400-163767200	Enhancers	HSMMtube	muscle
26	chr6:163766600-163767600	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
27	chr6:163766800-163768200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr6:163766800-163768400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
29	chr6:163766800-163768600	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
30	chr6:163767000-163767200	Enhancers	Brain Germinal Matrix	brain
31	chr6:163767000-163767200	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
32	chr6:163767000-163767200	Enhancers	Esophagus	oesophagus
33	chr6:163767000-163767400	Flanking Active TSS	Fetal Muscle Trunk	muscle
34	chr6:163767000-163767600	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
35	chr6:163767000-163767600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
36	chr6:163767000-163767600	Enhancers	Psoas Muscle	Psoas
37	chr6:163767000-163767600	Enhancers	HSMM	muscle
38	chr6:163767000-163768200	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
39	chr6:163767000-163768200	Enhancers	Fetal Brain Female	brain
40	chr6:163767000-163768400	Enhancers	Left Ventricle	heart
41	chr6:163767000-163768400	Enhancers	Right Atrium	heart
42	chr6:163767000-163768600	Enhancers	Placenta	Placenta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links