Variant report

Variant	rs11265489
Chromosome Location	chr1:160777548-160777549
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr1:160777520-160777670	GM12870	blood:	n/a	n/a
2	CTCF	chr1:160777540-160777690	GM12874	blood:	n/a	n/a
3	CTCF	chr1:160777480-160777630	GM06990	blood:	n/a	n/a

Variant related genes	Relation type
LY9	TF binding region

Extended variants
information (count: 25 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:22)

rs_ID	r²[population]
rs11265487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs11265488	1.00[CEU][hapmap];0.91[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2779800	0.85[CEU][hapmap]
rs4017732	1.00[YRI][hapmap];0.82[AFR][1000 genomes]
rs474131	0.85[CEU][hapmap]
rs492874	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs492906	0.84[AMR][1000 genomes];0.82[EUR][1000 genomes]
rs494091	0.85[CEU][hapmap]
rs496201	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs506081	0.85[CEU][hapmap]
rs509749	0.85[CEU][hapmap]
rs510143	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs516509	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs522897	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs539433	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs551827	0.85[CEU][hapmap]
rs556810	0.86[CEU][hapmap]
rs567306	0.82[CEU][hapmap]
rs569659	0.92[CEU][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs571841	0.86[CEU][hapmap]
rs6427548	1.00[CEU][hapmap];0.95[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs6667581	1.00[CEU][hapmap];0.94[YRI][hapmap];0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[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	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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs11265489	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs11265489	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:28 , 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	chr1:160772400-160777600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr1:160774400-160782400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
5	chr1:160775400-160778400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:160775600-160783000	Weak transcription	Duodenum Mucosa	Duodenum
7	chr1:160776200-160777800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
8	chr1:160776800-160780200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:160777000-160778000	ZNF genes & repeats	Fetal Thymus	thymus
10	chr1:160777000-160778000	ZNF genes & repeats	Thymus	Thymus
11	chr1:160777200-160777600	ZNF genes & repeats	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:160777200-160777600	Genic enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr1:160777200-160777600	ZNF genes & repeats	Gastric	stomach
14	chr1:160777200-160777800	Genic enhancers	Primary T cells from cord blood	blood
15	chr1:160777200-160777800	Genic enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr1:160777200-160778000	ZNF genes & repeats	Spleen	Spleen
17	chr1:160777200-160778400	Genic enhancers	Primary T regulatory cells fromperipheralblood	blood
18	chr1:160777200-160778600	Genic enhancers	Primary T helper cells fromperipheralblood	blood
19	chr1:160777200-160781200	Genic enhancers	Primary T cells fromperipheralblood	blood
20	chr1:160777400-160777800	ZNF genes & repeats	Esophagus	oesophagus
21	chr1:160777400-160777800	Bivalent Enhancer	Placenta	Placenta
22	chr1:160777400-160778000	Genic enhancers	Primary B cells from peripheral blood	blood
23	chr1:160777400-160778000	ZNF genes & repeats	GM12878-XiMat	blood
24	chr1:160777400-160778400	Enhancers	Primary T helper naive cells from peripheral blood	blood
25	chr1:160777400-160778600	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr1:160777400-160778600	Genic enhancers	Primary mononuclear cells fromperipheralblood	Blood
27	chr1:160777400-160780400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr1:160777400-160789000	Strong transcription	Primary B cells from cord blood	blood

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