Variant report

Variant	rs7578356
Chromosome Location	chr2:38862223-38862224
allele	A/C
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:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr2:38860089..38863428-chr2:38976891..38979875,4	K562	blood:
2	chr2:38853457..38857426-chr2:38859030..38862948,5	K562	blood:
3	chr2:38861742..38863889-chr2:38865469..38867826,3	K562	blood:
4	chr2:38841845..38846119-chr2:38859783..38862280,3	K562	blood:
5	chr2:38861872..38863650-chr2:38976891..38979789,2	K562	blood:
6	chr2:38829210..38832278-chr2:38859055..38864456,6	K562	blood:
7	chr2:38826787..38832652-chr2:38859055..38867252,11	K562	blood:
8	chr2:38861742..38863266-chr2:38865469..38867826,2	K562	blood:

No data

No data

No data

Variant related genes	Relation type
ENSG00000115875	Chromatin interaction
ENSG00000152147	Chromatin interaction
ENSG00000235586	Chromatin interaction
ENSG00000143889	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:18)

rs_ID	r²[population]
rs11899756	1.00[MEX][hapmap]
rs12614876	1.00[CHB][hapmap];1.00[CHD][hapmap];0.85[JPT][hapmap];0.85[ASN][1000 genomes]
rs12616367	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12619629	1.00[CHB][hapmap];1.00[JPT][hapmap]
rs12621788	0.87[ASN][1000 genomes]
rs13398507	0.95[ASN][1000 genomes]
rs17022945	1.00[MEX][hapmap]
rs17576044	1.00[CHB][hapmap]
rs17603782	0.82[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs3765001	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs41446253	1.00[MEX][hapmap]
rs6732743	1.00[MEX][hapmap]
rs72913653	1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs72913657	0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs73930143	1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7579783	1.00[CHB][hapmap]
rs7584862	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[MEX][hapmap]
rs7606515	1.00[CHB][hapmap]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916059	chr2:38332341-39119398	Weak transcription Flanking Active TSS Enhancers Genic enhancers Strong transcription Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	143 gene(s)	inside rSNPs	diseases
2	nsv9646	chr2:38358311-39082189	Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Weak transcription Strong transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	141 gene(s)	inside rSNPs	diseases
3	nsv873881	chr2:38745624-38877636	Enhancers Flanking Active TSS Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	19 gene(s)	inside rSNPs	diseases
4	nsv581483	chr2:38799820-38862223	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
5	nsv581484	chr2:38799820-38874177	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
6	nsv581485	chr2:38839323-38893660	Weak transcription Enhancers Flanking Active TSS Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases
7	nsv873882	chr2:38858669-38921498	Flanking Active TSS Strong transcription Weak transcription Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	7 gene(s)	inside rSNPs	diseases
8	esv2762495	chr2:38861095-38886391	Enhancers Weak transcription ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh	Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs7578356	GAP43	trans	lymphoblastoid	seeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:38835400-38862400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr2:38861000-38862400	Enhancers	Dnd41	blood
3	chr2:38861000-38862600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
4	chr2:38861000-38862600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr2:38861000-38862600	Enhancers	Fetal Adrenal Gland	Adrenal Gland
6	chr2:38861000-38862800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
7	chr2:38861000-38863600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
8	chr2:38861200-38862600	Enhancers	Primary hematopoietic stem cells	blood
9	chr2:38861200-38862800	Enhancers	Primary monocytes fromperipheralblood	blood
10	chr2:38861400-38862800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
11	chr2:38861400-38863000	Enhancers	K562	blood
12	chr2:38861800-38862600	Enhancers	Primary B cells from peripheral blood	blood
13	chr2:38861800-38862600	Enhancers	Primary T helper cells fromperipheralblood	blood
14	chr2:38861800-38862600	Enhancers	Fetal Thymus	thymus
15	chr2:38862000-38862400	Flanking Active TSS	GM12878-XiMat	blood
16	chr2:38862000-38862400	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
17	chr2:38862000-38862800	Enhancers	Primary B cells from cord blood	blood

Quick Search:

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

what's new

Quick links