Variant report

Variant	rs2870517
Chromosome Location	chr3:150973841-150973842
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:150973802..150976430-chr3:150980938..150983221,2	K562	blood:

Extended variants
information (count: 47 )
Associated
traits (count: 4 )

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

rs_ID	r²[population]
rs1352887	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1388622	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs1388623	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1388624	0.85[CHB][hapmap];0.88[JPT][hapmap]
rs1388626	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1466684	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1491978	0.86[CHB][hapmap];0.84[CHD][hapmap];0.93[JPT][hapmap]
rs1491979	0.85[CHB][hapmap];1.00[JPT][hapmap]
rs1491980	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs1491981	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap]
rs1873622	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs1907637	1.00[YRI][hapmap]
rs2046934	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2141631	0.88[CEU][hapmap];0.86[CHB][hapmap];1.00[YRI][hapmap];0.89[EUR][1000 genomes]
rs2172249	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs2904431	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3732764	1.00[JPT][hapmap]
rs3821667	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs3971191	0.93[CHB][hapmap];0.92[CHD][hapmap];1.00[JPT][hapmap]
rs3975403	0.84[CHB][hapmap];1.00[JPT][hapmap]
rs3975404	0.86[CHB][hapmap];0.84[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs4146770	0.86[JPT][hapmap]
rs4603933	1.00[YRI][hapmap]
rs4679802	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs4680275	0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs4680374	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6440731	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.92[ASN][1000 genomes]
rs6440732	1.00[CHB][hapmap];0.96[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs6763983	0.90[ASN][1000 genomes]
rs6769397	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6782212	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6790748	0.86[CHB][hapmap];1.00[JPT][hapmap]
rs6809388	0.92[JPT][hapmap]
rs6809699	0.84[GIH][hapmap]
rs6809705	0.85[JPT][hapmap];0.88[TSI][hapmap]
rs7611328	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.92[MEX][hapmap];1.00[MKK][hapmap];0.96[TSI][hapmap];1.00[YRI][hapmap];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7615865	0.86[CHB][hapmap];0.84[CHD][hapmap];1.00[JPT][hapmap]
rs7616382	1.00[YRI][hapmap]
rs7620353	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7621876	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs7633362	0.93[CHB][hapmap];1.00[JPT][hapmap]
rs9820422	0.93[CHB][hapmap];0.92[CHD][hapmap];0.84[GIH][hapmap];1.00[JPT][hapmap]
rs9849395	1.00[YRI][hapmap]
rs9877389	0.93[CHB][hapmap];0.89[CHD][hapmap];0.86[JPT][hapmap]

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

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs2870517	CLRN1	cis	parietal	SCAN
rs2870517	P2RY13	cis	cerebellum	SCAN
rs2870517	FAM194A	cis	parietal	SCAN
rs2870517	MME	cis	parietal	SCAN

Chromatin state (count:23 , 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	chr3:150946800-150983600	Weak transcription	Cortex derived primary cultured neurospheres	brain
3	chr3:150952800-150978400	Weak transcription	Primary neutrophils fromperipheralblood	blood
4	chr3:150953800-150983800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr3:150959600-150977800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr3:150959600-150978200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr3:150961200-150983600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr3:150965000-150980800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
9	chr3:150967000-150982600	Weak transcription	Gastric	stomach
10	chr3:150967200-150974200	Weak transcription	Fetal Lung	lung
11	chr3:150969800-150977000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
12	chr3:150970600-150974200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr3:150971000-150975200	Weak transcription	Pancreatic Islets	Pancreatic Islet
14	chr3:150971000-150975400	Enhancers	Fetal Stomach	stomach
15	chr3:150971200-150983800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
16	chr3:150971400-150974000	Weak transcription	Stomach Mucosa	stomach
17	chr3:150971800-150978000	Enhancers	Rectal Smooth Muscle	rectum
18	chr3:150972000-150976400	Strong transcription	Primary B cells from cord blood	blood
19	chr3:150972800-150974200	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr3:150973600-150978400	Enhancers	Colon Smooth Muscle	Colon
21	chr3:150973800-150974000	Enhancers	HUES64 Cell Line	embryonic stem cell
22	chr3:150973800-150976200	Enhancers	Stomach Smooth Muscle	stomach
23	chr3:150973800-150983800	Weak transcription	HUES48 Cell Line	embryonic stem cell

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