Variant report

Variant	rs501137
Chromosome Location	chr1:160776642-160776643
allele	C/T
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	CBX3	chr1:160776596-160776970	K562	blood:	n/a	n/a
2	KAP1	chr1:160776408-160776989	K562	blood:	n/a	n/a
3	SETDB1	chr1:160776091-160777057	U2OS	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160769451..160770985-chr1:160774299..160776734,2	K562	blood:

Variant related genes	Relation type
LY9	TF binding region

Extended variants
information (count: 52 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:48)

rs_ID	r²[population]
rs10908806	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs11265484	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265485	1.00[CEU][hapmap];0.91[CHB][hapmap];0.85[JPT][hapmap];0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265498	0.81[JPT][hapmap]
rs12038600	0.81[JPT][hapmap]
rs12039896	0.81[JPT][hapmap]
rs12039959	0.81[JPT][hapmap]
rs12040152	0.83[JPT][hapmap]
rs12048113	0.83[JPT][hapmap]
rs12072397	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12072399	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1333064	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1855188	0.82[JPT][hapmap]
rs2769587	0.90[AMR][1000 genomes];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34002161	0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3766378	0.87[JPT][hapmap]
rs4656931	0.81[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4656934	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4656940	0.81[JPT][hapmap]
rs480104	0.85[CEU][hapmap];0.82[CHB][hapmap];1.00[JPT][hapmap];0.80[ASN][1000 genomes]
rs482921	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs489442	0.81[ASN][1000 genomes]
rs501026	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs506263	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508578	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs512197	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs520316	0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs527253	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs527766	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs535241	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs536015	0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs540224	1.00[CEU][hapmap];0.91[CHB][hapmap];0.86[JPT][hapmap];0.81[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs546669	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs560681	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.88[YRI][hapmap];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs575217	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.89[YRI][hapmap];0.82[AFR][1000 genomes];0.90[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs579589	1.00[CEU][hapmap];0.91[CHB][hapmap];1.00[JPT][hapmap];0.85[YRI][hapmap];0.88[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6427544	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6427545	1.00[CEU][hapmap];0.95[CHB][hapmap];0.90[JPT][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6656939	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]
rs6691072	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7419088	0.82[JPT][hapmap]
rs7419110	0.83[JPT][hapmap]
rs7419145	0.82[JPT][hapmap]
rs7541298	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7553107	0.80[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7555137	0.82[EUR][1000 genomes]
rs7555286	1.00[CEU][hapmap];0.80[JPT][hapmap];0.94[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs790624	0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.99[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs501137	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:25 , 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	chr1:160771600-160777400	Genic enhancers	Primary T helper naive cells from peripheral blood	blood
3	chr1:160771800-160777200	Weak transcription	Gastric	stomach
4	chr1:160772200-160782000	Genic enhancers	Primary T helper naive cells fromperipheralblood	blood
5	chr1:160772400-160777000	Weak transcription	Thymus	Thymus
6	chr1:160772400-160777200	Weak transcription	Spleen	Spleen
7	chr1:160772400-160777600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
8	chr1:160773200-160777000	Weak transcription	Fetal Thymus	thymus
9	chr1:160773600-160777200	ZNF genes & repeats	Primary T cells from cord blood	blood
10	chr1:160774400-160782400	Genic enhancers	Primary T helper cells PMA-I stimulated	--
11	chr1:160775400-160777200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
12	chr1:160775400-160777200	ZNF genes & repeats	Primary T cells fromperipheralblood	blood
13	chr1:160775400-160777200	ZNF genes & repeats	Primary mononuclear cells fromperipheralblood	Blood
14	chr1:160775400-160777400	ZNF genes & repeats	Primary B cells from cord blood	blood
15	chr1:160775400-160777400	ZNF genes & repeats	Primary B cells from peripheral blood	blood
16	chr1:160775400-160778400	Genic enhancers	Primary T helper 17 cells PMA-I stimulated	--
17	chr1:160775600-160783000	Weak transcription	Duodenum Mucosa	Duodenum
18	chr1:160775800-160777200	ZNF genes & repeats	Primary T regulatory cells fromperipheralblood	blood
19	chr1:160776000-160777200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
20	chr1:160776000-160777400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
21	chr1:160776200-160777400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
22	chr1:160776200-160777800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
23	chr1:160776400-160776800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
24	chr1:160776600-160777200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
25	chr1:160776600-160777200	Strong transcription	Primary T helper cells fromperipheralblood	blood

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