Variant report

Variant	rs4656932
Chromosome Location	chr1:160779495-160779496
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 19 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11265492	0.95[AFR][1000 genomes];0.93[AMR][1000 genomes];0.90[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12117689	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12128261	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs12143580	0.86[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1556517	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs1961611	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2271967	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs35132864	0.82[AFR][1000 genomes];0.94[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3766377	0.85[CEU][hapmap];0.83[MEX][hapmap];0.90[TSI][hapmap]
rs3817407	0.95[CEU][hapmap];0.87[MEX][hapmap];0.93[TSI][hapmap];0.96[EUR][1000 genomes]
rs3904492	1.00[LWK][hapmap];1.00[MKK][hapmap];1.00[YRI][hapmap]
rs4656270	1.00[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4656271	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4656933	0.95[CEU][hapmap];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs4656942	1.00[ASW][hapmap];1.00[LWK][hapmap];0.84[MEX][hapmap];0.86[AFR][1000 genomes]
rs474918	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.98[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:8)

SNP	Gene	Cis/trans	Tissue	Source
rs4656932	PPOX	cis	cerebellum	SCAN
rs4656932	LMNA	cis	cerebellum	SCAN
rs4656932	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs4656932	PMF1	cis	parietal	SCAN
rs4656932	ISG20L2	cis	parietal	SCAN
rs4656932	CD244	cis	lymphoblastoid	seeQTL
rs4656932	ISG20L2	cis	cerebellum	SCAN
rs4656932	MRPL24	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160771000-160806600	Weak transcription	Rectal Mucosa Donor 29	rectum
2	chr1:160772200-160782000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
3	chr1:160774400-160782400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
4	chr1:160775600-160783000	Weak transcription	Duodenum Mucosa	Duodenum
5	chr1:160776800-160780200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
6	chr1:160777200-160781200	Genic enhancers	Primary T cells fromperipheralblood	blood
7	chr1:160777400-160780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
8	chr1:160777400-160789000	Strong transcription	Primary B cells from cord blood	blood
9	chr1:160777600-160783400	Weak transcription	Gastric	stomach
10	chr1:160777800-160779800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
11	chr1:160777800-160780800	Weak transcription	Esophagus	oesophagus
12	chr1:160778000-160780800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
13	chr1:160778000-160782800	Weak transcription	GM12878-XiMat	blood
14	chr1:160778000-160783000	Weak transcription	Fetal Thymus	thymus
15	chr1:160778000-160783000	Weak transcription	Thymus	Thymus
16	chr1:160778000-160783800	Weak transcription	Spleen	Spleen
17	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
18	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
19	chr1:160778400-160779800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr1:160778400-160780000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
21	chr1:160778400-160780800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr1:160778400-160783200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
23	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
24	chr1:160778600-160779600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr1:160778600-160779800	Weak transcription	Primary T cells from cord blood	blood
26	chr1:160778600-160780400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:160778600-160780600	Strong transcription	Primary T helper cells fromperipheralblood	blood
28	chr1:160778600-160783200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr1:160779000-160780000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
30	chr1:160779200-160780800	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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