Variant report

Variant	rs12998320
Chromosome Location	chr2:172237268-172237269
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 11 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs11674632	1.00[GIH][hapmap];0.81[MEX][hapmap]
rs11679835	1.00[GIH][hapmap]
rs11687454	0.96[GIH][hapmap]
rs11902733	0.98[AFR][1000 genomes];0.82[AMR][1000 genomes]
rs13000846	0.96[GIH][hapmap]
rs13023973	1.00[GIH][hapmap]
rs13031794	1.00[GIH][hapmap];0.81[MEX][hapmap]
rs2111459	1.00[GIH][hapmap];0.81[MEX][hapmap]
rs6722670	0.96[GIH][hapmap]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3382346	chr2:172062677-172363892	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	29 gene(s)	inside rSNPs	diseases
2	nsv1003130	chr2:172189196-172237268	ZNF genes & repeats Enhancers Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS	TF binding region CpG island Chromatin interactive region	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs12998320	HAT1	cis	parietal	SCAN
rs12998320	CDCA7	cis	cerebellum	SCAN
rs12998320	MAP1D	cis	parietal	SCAN
rs12998320	LASS6	cis	parietal	SCAN

Chromatin state (count:18 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:172211000-172242600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:172222200-172289600	Weak transcription	Gastric	stomach
3	chr2:172222400-172240200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
4	chr2:172223000-172242000	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
5	chr2:172229400-172246800	Weak transcription	NH-A	brain
6	chr2:172231400-172248000	Weak transcription	Skeletal Muscle Male	skeletal muscle
7	chr2:172231800-172239000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr2:172231800-172240800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
9	chr2:172231800-172243200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
10	chr2:172231800-172248200	Weak transcription	Esophagus	oesophagus
11	chr2:172232000-172253200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
12	chr2:172232200-172238800	Weak transcription	Liver	Liver
13	chr2:172232200-172242000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
14	chr2:172232600-172242000	Weak transcription	H1 Cell Line	embryonic stem cell
15	chr2:172232800-172241800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
16	chr2:172235400-172237800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
17	chr2:172235400-172244600	Weak transcription	Cortex derived primary cultured neurospheres	brain
18	chr2:172235600-172243400	Weak transcription	Primary hematopoietic stem cells	blood

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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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