Variant report

Variant	rs6656939
Chromosome Location	chr1:160773346-160773347
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 42 )
Associated
traits (count: 6 )

rSNPs within LD-proxies of this variant (count:38)

rs_ID	r²[population]
rs10908806	0.81[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265484	0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265485	1.00[CEU][hapmap];0.86[CHB][hapmap];0.93[CHD][hapmap];0.89[GIH][hapmap];0.81[JPT][hapmap];0.95[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12072397	0.83[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12072399	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1333064	0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2769587	0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34002161	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766378	0.81[JPT][hapmap]
rs4656931	0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656934	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs480104	0.85[CEU][hapmap];0.81[CHB][hapmap];0.95[JPT][hapmap];0.80[ASN][1000 genomes]
rs482921	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs489442	0.81[ASN][1000 genomes]
rs501026	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs501137	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.89[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506263	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508578	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs512197	0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs520316	0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527253	0.83[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527766	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs535241	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs536015	0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs540224	1.00[CEU][hapmap];0.86[CHB][hapmap];0.81[JPT][hapmap];0.88[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs546669	0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560681	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.95[MEX][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575217	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[JPT][hapmap];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579589	1.00[CEU][hapmap];0.91[CHB][hapmap];0.95[CHD][hapmap];1.00[GIH][hapmap];0.95[JPT][hapmap];0.85[MEX][hapmap];1.00[TSI][hapmap];0.81[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427544	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427545	1.00[CEU][hapmap];0.91[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];0.86[JPT][hapmap];1.00[MEX][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6685774	0.81[EUR][1000 genomes]
rs6691072	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.93[YRI][hapmap];0.93[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7541298	0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553107	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555137	0.82[EUR][1000 genomes]
rs7555286	1.00[CEU][hapmap];0.81[GIH][hapmap];0.86[MEX][hapmap];0.97[TSI][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs790624	0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[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	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	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
4	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
rs6656939	SMG5	cis	cerebellum	SCAN
rs6656939	PPOX	cis	cerebellum	SCAN
rs6656939	CLK2	cis	parietal	SCAN
rs6656939	SNORA42	cis	cerebellum	SCAN
rs6656939	SLAMF6	cis	cerebellum	SCAN
rs6656939	CASQ1	cis	parietal	SCAN

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160768600-160774000	Genic enhancers	Primary B cells from peripheral blood	blood
2	chr1:160771000-160774400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
3	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:160771200-160773800	Genic enhancers	Primary T cells fromperipheralblood	blood
5	chr1:160771200-160775400	Weak transcription	Duodenum Mucosa	Duodenum
6	chr1:160771400-160775600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
7	chr1:160771600-160773600	Genic enhancers	Primary T helper memory cells from peripheral blood 2	blood
8	chr1:160771600-160774000	Genic enhancers	Primary T helper cells PMA-I stimulated	--
9	chr1:160771600-160777400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
10	chr1:160771800-160777200	Weak transcription	Gastric	stomach
11	chr1:160772200-160773800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
12	chr1:160772200-160782000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
13	chr1:160772400-160775600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
14	chr1:160772400-160776200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
15	chr1:160772400-160777000	Weak transcription	Thymus	Thymus
16	chr1:160772400-160777200	Weak transcription	Spleen	Spleen
17	chr1:160772400-160777600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
18	chr1:160772800-160773400	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
19	chr1:160772800-160776000	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:160773000-160773400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr1:160773000-160775400	Strong transcription	Primary B cells from cord blood	blood
22	chr1:160773000-160775400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
23	chr1:160773200-160773600	Genic enhancers	Primary T cells from cord blood	blood
24	chr1:160773200-160777000	Weak transcription	Fetal Thymus	thymus

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