Variant report

Variant	rs489651
Chromosome Location	chr1:160820980-160820981
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs11265493	0.84[CEU][hapmap];0.95[CHB][hapmap];0.86[CHD][hapmap];0.91[JPT][hapmap];0.88[ASN][1000 genomes]
rs11265496	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs11582719	1.00[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs11587898	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs1319651	1.00[CEU][hapmap];0.98[EUR][1000 genomes]
rs2139660	0.84[CEU][hapmap];0.86[CHB][hapmap];0.86[JPT][hapmap];0.84[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs2280415	0.96[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2779790	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2779792	0.97[EUR][1000 genomes]
rs2990702	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2990703	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs3753389	0.96[CEU][hapmap];0.95[CHB][hapmap];0.93[CHD][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3766379	0.96[CEU][hapmap];0.95[CHB][hapmap];0.95[CHD][hapmap];1.00[JPT][hapmap];0.96[TSI][hapmap];0.87[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4656936	0.89[ASN][1000 genomes]
rs4656937	0.96[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.81[YRI][hapmap];0.84[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4656938	0.96[CEU][hapmap];0.95[CHB][hapmap];0.88[CHD][hapmap];0.87[GIH][hapmap];1.00[JPT][hapmap];0.92[LWK][hapmap];0.95[MEX][hapmap];0.82[MKK][hapmap];0.95[TSI][hapmap];0.81[YRI][hapmap];0.87[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs483197	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs491061	0.96[CEU][hapmap];0.89[EUR][1000 genomes]
rs499721	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs512525	1.00[CEU][hapmap];0.87[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs535610	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs536906	0.96[EUR][1000 genomes]
rs537957	0.97[EUR][1000 genomes]
rs541834	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs549565	1.00[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs578608	0.94[EUR][1000 genomes]
rs60755678	0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6671710	1.00[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.96[EUR][1000 genomes]
rs6682654	1.00[CEU][hapmap];0.83[MEX][hapmap];0.98[TSI][hapmap];0.97[EUR][1000 genomes]
rs7518342	0.84[CEU][hapmap];0.95[CHB][hapmap];0.91[JPT][hapmap];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 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	nsv464161	chr1:160747615-160852046	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv548057	chr1:160747615-160852046	Weak transcription Genic enhancers Enhancers Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
4	nsv946456	chr1:160812650-160824679	Enhancers Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region	2 gene(s)	inside rSNPs	diseases

mRNA abundance (count:7)

SNP	Gene	Cis/trans	Tissue	Source
rs489651	RXFP4	cis	parietal	SCAN
rs489651	CD244	cis	lymphoblastoid	seeQTL
rs489651	ISG20L2	cis	cerebellum	SCAN
rs489651	CD244	Cis_1M	lymphoblastoid	RTeQTL
rs489651	FCGR2B	cis	parietal	SCAN
rs489651	CD5L	cis	parietal	SCAN
rs489651	PPOX	cis	cerebellum	SCAN

Chromatin state (count:16 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160811800-160824600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
2	chr1:160812800-160824200	Weak transcription	Thymus	Thymus
3	chr1:160817800-160821200	Strong transcription	Primary hematopoietic stem cells short term culture	blood
4	chr1:160817800-160825400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160819200-160821200	Enhancers	Primary T cells fromperipheralblood	blood
6	chr1:160819200-160823200	Weak transcription	Primary hematopoietic stem cells	blood
7	chr1:160819400-160822400	Weak transcription	Primary monocytes fromperipheralblood	blood
8	chr1:160820200-160821000	Enhancers	Primary T killer memory cells from peripheral blood	blood
9	chr1:160820200-160821200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
10	chr1:160820200-160821600	Enhancers	Fetal Intestine Large	intestine
11	chr1:160820200-160821800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr1:160820400-160821000	Enhancers	Duodenum Mucosa	Duodenum
13	chr1:160820400-160821200	Enhancers	Fetal Intestine Small	intestine
14	chr1:160820600-160821200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr1:160820800-160821000	Enhancers	Spleen	Spleen
16	chr1:160820800-160821200	Strong transcription	Monocytes-CD14+_RO01746	blood

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