Variant report

Variant	rs12996834
Chromosome Location	chr2:55063905-55063906
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 16 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:9)

rs_ID	r²[population]
rs10173697	0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.93[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10205156	0.87[AFR][1000 genomes];0.99[ASN][1000 genomes]
rs10208786	1.00[CHB][hapmap];0.98[CHD][hapmap];0.89[GIH][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs12713277	0.94[ASN][1000 genomes]
rs12999197	0.90[ASN][1000 genomes]
rs1465673	0.89[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs1549840	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2358153	0.90[ASN][1000 genomes]
rs930493	0.92[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	esv33638	chr2:54765256-55109455	Enhancers Weak transcription Genic enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	29 gene(s)	inside rSNPs	diseases
2	nsv1005449	chr2:54938633-55129503	Flanking Active TSS Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
3	esv1844727	chr2:54999712-55084583	Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv870295	chr2:55008613-55065985	Enhancers Bivalent Enhancer Flanking Active TSS Weak transcription Active TSS	Chromatin interactive region lncRNA	2 gene(s)	inside rSNPs	diseases
5	nsv874153	chr2:55042463-55073428	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
6	nsv525624	chr2:55063113-55066310	Weak transcription Enhancers	Chromatin interactive region	1 gene(s)	inside rSNPs	diseases
7	nsv874154	chr2:55063113-55084583	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12996834	CCDC85A	cis	cerebellum	SCAN
rs12996834	SUPV3L1	trans	parietal	SCAN

Chromatin state (count:17 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55046400-55065600	Weak transcription	Primary B cells from peripheral blood	blood
2	chr2:55053400-55079000	Weak transcription	HepG2	liver
3	chr2:55053600-55065000	Weak transcription	Brain Inferior Temporal Lobe	brain
4	chr2:55053600-55065200	Weak transcription	Brain Angular Gyrus	brain
5	chr2:55054200-55067200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
6	chr2:55057600-55064600	Weak transcription	Brain Substantia Nigra	brain
7	chr2:55062200-55069600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:55062400-55065600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr2:55062400-55066600	Weak transcription	HSMMtube	muscle
10	chr2:55062600-55066600	Weak transcription	Ovary	ovary
11	chr2:55063000-55064000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
12	chr2:55063400-55064000	Enhancers	Placenta	Placenta
13	chr2:55063600-55064000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
14	chr2:55063600-55064200	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
15	chr2:55063800-55064000	Enhancers	Fetal Muscle Leg	muscle
16	chr2:55063800-55064400	Enhancers	Adipose Nuclei	Adipose
17	chr2:55063800-55072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived

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dbSNP/dbVar ID: rs12345 /nsv7879
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chromosomal regions: chr1:12345-34567

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