Variant report

Variant	rs969788
Chromosome Location	chr1:86916856-86916857
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 13 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10493791	0.81[ASW][hapmap]
rs11161808	0.84[JPT][hapmap]
rs11161827	0.81[AFR][1000 genomes]
rs11161828	0.81[ASW][hapmap]
rs11161830	0.81[ASW][hapmap]
rs11161833	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11800629	0.81[ASW][hapmap]
rs12747430	0.84[JPT][hapmap]
rs1413426	1.00[ASW][hapmap];0.85[YRI][hapmap]
rs2390059	0.80[ASW][hapmap]
rs3737671	0.84[JPT][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	nsv1003838	chr1:86591841-87212231	Flanking Bivalent TSS/Enh Enhancers Weak transcription Flanking Active TSS Genic enhancers Active TSS Strong transcription Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	nsv521366	chr1:86916767-86922161	Enhancers Weak transcription Strong transcription	Chromatin interactive region	n/a	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs969788	SSX2IP	cis	cerebellum	SCAN
rs969788	BCL10	cis	parietal	SCAN
rs969788	ODF2L	cis	cerebellum	SCAN

Chromatin state (count:13 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:86897200-86922600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
2	chr1:86897200-86922800	Strong transcription	HMEC	breast
3	chr1:86903400-86926800	Weak transcription	Esophagus	oesophagus
4	chr1:86914400-86917000	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
5	chr1:86914600-86930800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr1:86915200-86920000	Strong transcription	NHEK	skin
7	chr1:86915400-86917400	Enhancers	HUVEC	blood vessel
8	chr1:86915600-86919400	Weak transcription	K562	blood
9	chr1:86916400-86917000	Enhancers	Dnd41	blood
10	chr1:86916400-86917400	Enhancers	iPS-15b Cell Line	embryonic stem cell
11	chr1:86916400-86921600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr1:86916800-86917200	Enhancers	HUES6 Cell Line	embryonic stem cell
13	chr1:86916800-86917400	Enhancers	Primary hematopoietic stem cells short term culture	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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