Variant report

Variant	rs4671978
Chromosome Location	chr2:55070508-55070509
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs17046413	0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs17046514	0.82[CEU][hapmap]
rs4671232	0.85[EUR][1000 genomes]
rs4671981	0.81[EUR][1000 genomes]
rs4671982	0.81[EUR][1000 genomes]
rs4671993	0.82[CEU][hapmap]
rs6716399	0.90[ASN][1000 genomes]
rs723975	0.81[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	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
5	nsv874154	chr2:55063113-55084583	Enhancers Weak transcription	TF binding region Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs4671978	CCDC104	cis	brain	BrainEAC

Chromatin state (count:14 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:55053400-55079000	Weak transcription	HepG2	liver
2	chr2:55063800-55072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
3	chr2:55065800-55071200	Weak transcription	Fetal Brain Male	brain
4	chr2:55066400-55072400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr2:55066800-55084400	Weak transcription	HSMMtube	muscle
6	chr2:55066800-55088800	Weak transcription	Brain Substantia Nigra	brain
7	chr2:55067200-55072200	Weak transcription	Pancreatic Islets	Pancreatic Islet
8	chr2:55068400-55096200	Weak transcription	Brain Cingulate Gyrus	brain
9	chr2:55068400-55109000	Weak transcription	Brain Inferior Temporal Lobe	brain
10	chr2:55068600-55072000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
11	chr2:55068600-55122400	Weak transcription	Brain Anterior Caudate	brain
12	chr2:55068800-55072600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr2:55069200-55070600	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
14	chr2:55070400-55077200	Weak transcription	NHEK	skin

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Input of quick search could be:

dbSNP/dbVar ID: rs12345 /nsv7879
a single nucleotide as 0-based coordinates: chr1:12345
chromosomal regions: chr1:12345-34567

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