Variant report

Variant	rs3766373
Chromosome Location	chr1:160714724-160714725
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11265473	0.92[CEU][hapmap];1.00[CHB][hapmap];0.85[JPT][hapmap];0.88[EUR][1000 genomes]
rs11588524	1.00[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17313034	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[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];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17313062	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2090756	1.00[ASN][1000 genomes]
rs2295616	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs35967351	0.90[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3766370	1.00[CEU][hapmap];0.86[MEX][hapmap];0.81[MKK][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3766374	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3845628	0.98[ASN][1000 genomes]
rs489286	0.84[CEU][hapmap];0.87[TSI][hapmap]
rs495706	0.80[CEU][hapmap];0.84[TSI][hapmap]
rs518721	0.84[CEU][hapmap];0.84[TSI][hapmap]
rs66692283	0.96[ASN][1000 genomes]
rs72710704	1.00[ASN][1000 genomes]
rs983494	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	esv1822379	chr1:160545332-160831143	Enhancers Active TSS Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	23 gene(s)	inside rSNPs	diseases
2	nsv831714	chr1:160581168-160776809	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
3	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs3766373	RXFP4	cis	parietal	SCAN
rs3766373	SLAMF7	cis	multi-tissue	Pritchard
rs3766373	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs3766373	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs3766373	SLAMF7	cis	lymphoblastoid	seeQTL
rs3766373	OR10J3	cis	cerebellum	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160708200-160715200	Enhancers	Primary monocytes fromperipheralblood	blood
2	chr1:160709400-160718400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
3	chr1:160711000-160715000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
4	chr1:160711200-160717200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:160711400-160715400	Enhancers	Primary T helper cells fromperipheralblood	blood
6	chr1:160711600-160715200	Enhancers	Fetal Thymus	thymus
7	chr1:160711600-160715200	Enhancers	Thymus	Thymus
8	chr1:160712000-160715400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
9	chr1:160712000-160716600	Weak transcription	HUES6 Cell Line	embryonic stem cell
10	chr1:160712200-160716400	Weak transcription	H9 Cell Line	embryonic stem cell
11	chr1:160712800-160715200	Enhancers	Monocytes-CD14+_RO01746	blood
12	chr1:160712800-160718000	Enhancers	Primary T cells fromperipheralblood	blood
13	chr1:160713000-160720400	Weak transcription	Rectal Mucosa Donor 29	rectum
14	chr1:160713200-160715400	Enhancers	Primary T helper cells PMA-I stimulated	--
15	chr1:160713600-160714800	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
16	chr1:160713600-160715000	Weak transcription	Lung	lung
17	chr1:160713600-160718200	Weak transcription	Spleen	Spleen
18	chr1:160713800-160715000	Flanking Active TSS	Primary T helper naive cells from peripheral blood	blood
19	chr1:160714000-160715000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:160714000-160715800	Flanking Active TSS	GM12878-XiMat	blood
21	chr1:160714000-160717400	Enhancers	iPS-20b Cell Line	embryonic stem cell
22	chr1:160714200-160716600	Enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:160714200-160717000	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:160714400-160715200	Enhancers	Duodenum Mucosa	Duodenum
25	chr1:160714400-160718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr1:160714400-160719800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:160714400-160726800	Weak transcription	Primary B cells from peripheral blood	blood
28	chr1:160714600-160715000	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr1:160714600-160715400	Enhancers	Primary T cells from cord blood	blood

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