Variant report

Variant	rs10889676
Chromosome Location	chr1:67722567-67722568
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 24 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs10489628	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap];0.90[ASN][1000 genomes]
rs10489629	0.86[CHB][hapmap];0.88[CHD][hapmap];0.84[JPT][hapmap]
rs10889673	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10889674	1.00[ASN][1000 genomes]
rs10889675	0.80[CHD][hapmap]
rs10889677	1.00[ASW][hapmap];1.00[CEU][hapmap];0.93[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11465802	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11465817	0.95[CEU][hapmap];0.88[TSI][hapmap]
rs12030107	0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12030948	0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.84[LWK][hapmap];0.96[ASN][1000 genomes]
rs12031203	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12567232	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12743974	1.00[ASN][1000 genomes]
rs1343152	0.93[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2180294	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2201841	0.91[CEU][hapmap];0.93[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.97[LWK][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs35380856	0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs35427944	0.86[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs4655529	0.90[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6665959	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs6686950	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6693831	0.89[CHD][hapmap]
rs7518660	0.85[CHD][hapmap]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1243	chr1:67700289-67745337	Weak transcription Enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer	TF binding region Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Crohn's disease	17804789	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs10889676	SAV1	trans	cerebellum	SCAN
rs10889676	STRA6	trans	cerebellum	SCAN

Chromatin state (count:19 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:67721800-67723200	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr1:67721800-67723200	Enhancers	Psoas Muscle	Psoas
3	chr1:67721800-67723600	Enhancers	iPS-15b Cell Line	embryonic stem cell
4	chr1:67722000-67722600	Weak transcription	HUES64 Cell Line	embryonic stem cell
5	chr1:67722000-67723000	Enhancers	HUES6 Cell Line	embryonic stem cell
6	chr1:67722000-67723000	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
7	chr1:67722000-67723000	Enhancers	HUVEC	blood vessel
8	chr1:67722000-67723200	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
9	chr1:67722000-67723200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr1:67722000-67723200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr1:67722000-67723200	Strong transcription	K562	blood
12	chr1:67722000-67723400	Enhancers	iPS-18 Cell Line	embryonic stem cell
13	chr1:67722200-67723000	Enhancers	Brain Inferior Temporal Lobe	brain
14	chr1:67722200-67723000	Enhancers	Fetal Lung	lung
15	chr1:67722200-67723200	Enhancers	H9 Cell Line	embryonic stem cell
16	chr1:67722200-67723200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
17	chr1:67722200-67723400	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr1:67722400-67726400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr1:67722400-67727400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--

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