Variant report

Variant	rs7568449
Chromosome Location	chr2:190521054-190521055
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:190519452..190521192-chr2:190525972..190527826,2	MCF-7	breast:
2	chr2:190515275..190516787-chr2:190520787..190523527,2	MCF-7	breast:
3	chr2:190518831..190521733-chr2:190570442..190572727,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000138381	Chromatin interaction

Extended variants
information (count: 55 )
Associated
traits (count: 21 )

rSNPs within LD-proxies of this variant (count:54)

rs_ID	r²[population]
rs10195109	0.87[JPT][hapmap]
rs10207346	0.82[ASN][1000 genomes]
rs1055091	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs10931430	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs10931431	0.83[ASN][1000 genomes]
rs1132360	0.94[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs11679767	0.89[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.89[ASN][1000 genomes]
rs1225101	0.91[JPT][hapmap]
rs1233245	0.89[CHB][hapmap];0.82[JPT][hapmap]
rs1233255	0.86[CEU][hapmap]
rs1233276	0.93[CEU][hapmap]
rs1233284	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs1233288	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs1233297	0.89[CHB][hapmap];0.86[CHD][hapmap];0.88[JPT][hapmap];0.85[TSI][hapmap]
rs1233302	0.94[CHB][hapmap];0.93[JPT][hapmap]
rs12471217	0.83[ASN][1000 genomes]
rs12471663	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12693551	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.93[LWK][hapmap];0.96[MKK][hapmap];0.88[TSI][hapmap];0.86[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12693557	0.94[CHB][hapmap];1.00[JPT][hapmap]
rs12990627	0.83[ASN][1000 genomes]
rs13011710	0.83[ASN][1000 genomes]
rs1437891	0.94[CHB][hapmap];0.94[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.84[ASN][1000 genomes]
rs1550388	0.87[JPT][hapmap]
rs16831873	0.86[CEU][hapmap]
rs1898560	0.81[JPT][hapmap]
rs1899025	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs2033870	0.94[CHB][hapmap];0.91[CHD][hapmap];1.00[JPT][hapmap];0.82[TSI][hapmap]
rs2278591	0.86[CEU][hapmap]
rs2289226	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];0.85[TSI][hapmap];0.92[YRI][hapmap];0.88[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs3791767	0.81[JPT][hapmap]
rs3791770	0.81[JPT][hapmap]
rs3791773	0.81[JPT][hapmap]
rs3816196	0.89[CHB][hapmap];0.88[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs4666783	0.87[JPT][hapmap]
rs4667296	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4667297	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.95[LWK][hapmap];1.00[MKK][hapmap];0.88[TSI][hapmap];0.92[YRI][hapmap];0.92[AFR][1000 genomes];0.91[ASN][1000 genomes]
rs4667299	0.89[ASN][1000 genomes]
rs5742938	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs5743047	0.86[CEU][hapmap]
rs5743061	0.83[CHD][hapmap];0.81[JPT][hapmap]
rs5743063	0.85[CHD][hapmap];0.81[JPT][hapmap]
rs61487110	0.95[AFR][1000 genomes];0.97[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs6434361	0.85[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs6434365	0.87[JPT][hapmap]
rs6756571	0.83[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6756913	0.90[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6761923	0.93[AFR][1000 genomes];0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs6942	0.94[CHB][hapmap];0.94[JPT][hapmap]
rs7557519	0.87[JPT][hapmap]
rs7571089	0.94[CHB][hapmap];1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs7577644	0.81[EUR][1000 genomes]
rs7591929	0.94[CHB][hapmap];0.91[CHD][hapmap];0.94[JPT][hapmap];0.88[TSI][hapmap]
rs893784	0.94[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.88[TSI][hapmap];0.90[ASN][1000 genomes]
rs9646811	0.89[CHB][hapmap];0.84[JPT][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.82[AMR][1000 genomes]

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	nsv533029	chr2:189812229-190554339	Active TSS Enhancers Weak transcription Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	40 gene(s)	inside rSNPs	diseases

mRNA abundance (count:21)

SNP	Gene	Cis/trans	Tissue	Source
rs7568449	ORMDL1	cis	Skin Sun Exposed Lower leg	GTEx
rs7568449	PMS1	cis	cerebellum	SCAN
rs7568449	PMS1	cis	parietal	SCAN
rs7568449	MFSD6	cis	cerebellum	SCAN
rs7568449	ORMDL1	cis	Adipose Subcutaneous	GTEx
rs7568449	ORMDL1	cis	uninvolved skin	skin_eQTL
rs7568449	HIBCH	cis	parietal	SCAN
rs7568449	ASNSD1	cis	Whole Blood	GTEx
rs7568449	PMS1	Cis_1M	lymphoblastoid	RTeQTL
rs7568449	ORMDL1	cis	normal skin	skin_eQTL
rs7568449	ORMDL1	cis	cerebellum	SCAN
rs7568449	ORMDL1	cis	parietal	SCAN
rs7568449	ORMDL1	cis	lymphoblastoid	seeQTL
rs7568449	ORMDL1	cis	lesional skin	skin_eQTL
rs7568449	ASNSD1	cis	cerebellum	SCAN
rs7568449	LOC51240	cis	multi-tissue	Pritchard
rs7568449	ORMDL1	Cis_1M	lymphoblastoid	RTeQTL
rs7568449	ASNSD1	Cis_1M	lymphoblastoid	RTeQTL
rs7568449	ORMDL1	cis	Lymphoblastoid	GTEx
rs7568449	ORMDL1	cis	multi-tissue	Pritchard
rs7568449	ASNSD1	cis	parietal	SCAN

Chromatin state (count:12 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:190506800-190522400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
2	chr2:190514800-190525600	Weak transcription	NHLF	lung
3	chr2:190520000-190522200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
4	chr2:190520000-190522400	Enhancers	Primary T cells from cord blood	blood
5	chr2:190520000-190525600	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
6	chr2:190520200-190526200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr2:190520800-190521800	Weak transcription	Primary T cells fromperipheralblood	blood
8	chr2:190520800-190522400	Enhancers	Primary T helper cells PMA-I stimulated	--
9	chr2:190521000-190521200	Enhancers	Fetal Thymus	thymus
10	chr2:190521000-190522000	Weak transcription	Primary T helper cells fromperipheralblood	blood
11	chr2:190521000-190522000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr2:190521000-190522200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood

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