Variant report

Variant	rs7978854
Chromosome Location	chr12:39771606-39771607
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:39768164..39770883-chr12:39771123..39773923,3	K562	blood:
2	chr12:39769582..39772161-chr12:39835841..39837638,2	K562	blood:
3	chr12:39770581..39773028-chr12:39775151..39777027,2	K562	blood:
4	chr12:39771043..39772683-chr12:39784560..39786078,2	MCF-7	breast:
5	chr12:39735428..39738305-chr12:39770401..39772553,2	K562	blood:

Variant related genes	Relation type
ENSG00000139116	Chromatin interaction
ENSG00000252974	Chromatin interaction

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

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1512941	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1512943	0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs17126997	0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs17127029	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127070	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127094	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127100	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17127129	0.83[ASN][1000 genomes]
rs17127138	0.83[ASN][1000 genomes]
rs2137495	0.95[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2271478	0.83[ASN][1000 genomes]
rs2292491	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4620763	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs57196300	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58891998	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs59967849	0.87[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61039034	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7135918	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307730	1.00[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7308138	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73086885	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73088816	0.83[ASN][1000 genomes]
rs7956823	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7966841	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970819	0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7970944	0.83[ASN][1000 genomes]
rs7976275	1.00[AFR][1000 genomes];0.96[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7980595	1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs963637	0.81[ASN][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	nsv832375	chr12:39599362-39784722	Enhancers Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
2	nsv832376	chr12:39633080-39808277	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
3	nsv531527	chr12:39680812-40182822	Enhancers Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:20 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:39697800-39771800	Weak transcription	Fetal Kidney	kidney
2	chr12:39727000-39779200	Weak transcription	Aorta	Aorta
3	chr12:39745000-39778600	Weak transcription	Pancreas	Pancrea
4	chr12:39751600-39771800	Weak transcription	Brain Anterior Caudate	brain
5	chr12:39757000-39784600	Weak transcription	Brain Germinal Matrix	brain
6	chr12:39761800-39806000	Weak transcription	Hela-S3	cervix
7	chr12:39763000-39781400	Weak transcription	A549	lung
8	chr12:39764000-39781000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
9	chr12:39765800-39772200	Weak transcription	Left Ventricle	heart
10	chr12:39767400-39784800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr12:39767600-39791400	Weak transcription	GM12878-XiMat	blood
12	chr12:39767800-39784800	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:39768000-39776800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr12:39769200-39771800	Weak transcription	Brain Angular Gyrus	brain
15	chr12:39770000-39772200	Weak transcription	Fetal Heart	heart
16	chr12:39770400-39772600	Enhancers	Cortex derived primary cultured neurospheres	brain
17	chr12:39771000-39772200	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:39771200-39772600	Enhancers	Pancreatic Islets	Pancreatic Islet
19	chr12:39771400-39772600	Enhancers	Brain Hippocampus Middle	brain
20	chr12:39771600-39772000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain

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