Variant report

Variant	rs6809692
Chromosome Location	chr3:150968515-150968516
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-GPR87-1	chr3:150968173-150968572	ucscGeneNc_uc003exl_1

Extended variants
information (count: 47 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:44)

rs_ID	r²[population]
rs10212582	0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1048408	0.87[CEU][hapmap]
rs10513392	0.88[CEU][hapmap]
rs11711104	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11714714	0.82[EUR][1000 genomes]
rs11719936	0.88[CEU][hapmap]
rs13317873	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1472122	0.87[CEU][hapmap]
rs1565574	0.86[CEU][hapmap]
rs1882014	0.87[CEU][hapmap]
rs1882015	0.88[CEU][hapmap]
rs1882016	0.87[CEU][hapmap]
rs1920395	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[ASN][1000 genomes]
rs1980143	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2904430	0.88[CEU][hapmap]
rs3846072	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4269062	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4679772	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4679783	0.82[EUR][1000 genomes]
rs4680254	0.82[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4680257	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680260	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.96[YRI][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680273	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6440730	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6782715	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs6807308	0.96[CEU][hapmap]
rs73021201	0.89[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7617677	0.96[CEU][hapmap]
rs7621113	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7621211	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7623448	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs7653603	0.95[CEU][hapmap];0.80[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs8180086	0.87[CEU][hapmap]
rs9757688	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs9810067	0.88[CEU][hapmap]
rs9815520	1.00[CEU][hapmap];1.00[CHB][hapmap];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs9827619	0.88[CEU][hapmap]
rs9828553	0.87[CEU][hapmap]
rs9829753	0.81[EUR][1000 genomes]
rs9835328	0.87[CEU][hapmap];0.91[CHB][hapmap];0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9853297	0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9870740	0.96[CEU][hapmap];0.82[EUR][1000 genomes]
rs9875152	0.88[CEU][hapmap]
rs9880339	0.87[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv460894	chr3:150770614-151095093	Enhancers Flanking Bivalent TSS/Enh Weak transcription Strong transcription Genic enhancers Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
2	nsv592045	chr3:150770614-151095093	Flanking Active TSS Weak transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
3	esv2754555	chr3:150968302-151054302	Enhancers Weak transcription Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:21 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:150946200-150979400	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
2	chr3:150946800-150969200	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
4	chr3:150952800-150978400	Weak transcription	Primary neutrophils fromperipheralblood	blood
5	chr3:150953800-150983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
6	chr3:150959400-150970600	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
7	chr3:150959600-150977800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
8	chr3:150959600-150978200	Weak transcription	Primary hematopoietic stem cells	blood
9	chr3:150961200-150983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr3:150965000-150980800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
11	chr3:150966400-150970600	Weak transcription	Rectal Smooth Muscle	rectum
12	chr3:150967000-150969200	Weak transcription	Stomach Mucosa	stomach
13	chr3:150967000-150971400	Weak transcription	Stomach Smooth Muscle	stomach
14	chr3:150967000-150982600	Weak transcription	Gastric	stomach
15	chr3:150967200-150969400	Enhancers	Pancreatic Islets	Pancreatic Islet
16	chr3:150967200-150974200	Weak transcription	Fetal Lung	lung
17	chr3:150967600-150968600	Weak transcription	Right Atrium	heart
18	chr3:150967600-150971000	Weak transcription	Fetal Stomach	stomach
19	chr3:150967800-150969400	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:150967800-150970600	Weak transcription	Colon Smooth Muscle	Colon
21	chr3:150968400-150968800	Strong transcription	Primary B cells from cord blood	blood

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