Variant report

Variant	rs12039959
Chromosome Location	chr1:160827379-160827380
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 55 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10908807	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs11265498	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.89[MEX][hapmap];1.00[TSI][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265499	0.82[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11265500	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265501	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12035295	0.85[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];0.91[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12035537	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12036607	0.85[CEU][hapmap];0.91[CHB][hapmap];0.85[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12036670	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037395	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12037740	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12037885	0.85[CEU][hapmap];0.82[CHB][hapmap];0.84[JPT][hapmap];0.85[YRI][hapmap];0.80[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs12038419	0.85[CEU][hapmap];0.86[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12038600	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12039896	1.00[ASW][hapmap];0.93[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.97[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];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040060	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs12040152	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12040750	0.95[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12046019	0.94[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12046021	0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12047127	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12048113	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1412849	0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1576964	0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855188	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1855189	0.83[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs3766378	0.81[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs4656940	0.85[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.85[LWK][hapmap];0.94[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];0.96[YRI][hapmap];0.84[AFR][1000 genomes];0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656941	0.84[CEU][hapmap];0.94[CHB][hapmap];0.93[JPT][hapmap];0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4656943	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.94[TSI][hapmap];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs480104	0.86[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs501026	0.81[JPT][hapmap]
rs501137	0.81[JPT][hapmap]
rs560681	0.81[JPT][hapmap]
rs57483437	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs575217	0.81[JPT][hapmap]
rs579589	0.81[JPT][hapmap]
rs58418513	0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs59712018	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61803263	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs61803285	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6691072	0.81[JPT][hapmap]
rs6698454	0.83[AFR][1000 genomes];0.97[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs72710762	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7410867	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.90[GIH][hapmap];0.85[JPT][hapmap];0.88[MEX][hapmap];0.97[TSI][hapmap];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs7412693	1.00[CEU][hapmap];0.95[CHB][hapmap];0.89[JPT][hapmap];0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7412696	0.87[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419088	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419110	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419145	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs955370	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs955371	0.85[CEU][hapmap];0.91[CHB][hapmap];0.83[CHD][hapmap];0.85[JPT][hapmap];0.83[MEX][hapmap];0.97[TSI][hapmap];0.80[AMR][1000 genomes];0.93[EUR][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	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

mRNA abundance (count:6)

SNP	Gene	Cis/trans	Tissue	Source
rs12039959	RHBG	cis	parietal	SCAN
rs12039959	CD244	Cis_1M	lymphoblastoid	RTeQTL
rs12039959	DEDD	cis	cerebellum	SCAN
rs12039959	CD5L	cis	parietal	SCAN
rs12039959	RXFP4	cis	parietal	SCAN
rs12039959	PPOX	cis	cerebellum	SCAN

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160821000-160828200	Weak transcription	Duodenum Mucosa	Duodenum
2	chr1:160821000-160830800	Weak transcription	Spleen	Spleen
3	chr1:160821600-160828000	Weak transcription	Fetal Intestine Large	intestine
4	chr1:160823000-160829000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
5	chr1:160824600-160831200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
6	chr1:160825200-160830600	Enhancers	Primary hematopoietic stem cells	blood
7	chr1:160825400-160827800	Genic enhancers	Monocytes-CD14+_RO01746	blood
8	chr1:160825800-160828800	Weak transcription	Primary neutrophils fromperipheralblood	blood
9	chr1:160826000-160827800	Weak transcription	Fetal Intestine Small	intestine
10	chr1:160826200-160827400	Enhancers	Primary hematopoietic stem cells short term culture	blood
11	chr1:160826200-160828000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
12	chr1:160826400-160830600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
13	chr1:160826400-160830800	Weak transcription	Primary T killer memory cells from peripheral blood	blood
14	chr1:160826400-160831800	Weak transcription	Primary T helper cells fromperipheralblood	blood
15	chr1:160826600-160827600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
16	chr1:160826600-160830200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
17	chr1:160826600-160830400	Enhancers	Primary T cells fromperipheralblood	blood
18	chr1:160826600-160832200	Weak transcription	Primary T helper cells PMA-I stimulated	--
19	chr1:160826800-160828600	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
20	chr1:160827000-160827400	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
21	chr1:160827000-160830600	Enhancers	Primary monocytes fromperipheralblood	blood

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