Variant report

Variant	rs6667581
Chromosome Location	chr1:160776541-160776542
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	KAP1	chr1:160776408-160776989	K562	blood:	n/a	n/a
2	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: 39 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs11265487	0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11265488	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11265489	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]
rs2027015	0.89[ASN][1000 genomes]
rs2779800	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs4017732	0.94[YRI][hapmap]
rs474131	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs485618	1.00[JPT][hapmap];0.84[ASN][1000 genomes]
rs492874	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs492906	0.80[AMR][1000 genomes];0.85[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs494091	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs496201	0.82[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs504848	0.86[ASN][1000 genomes]
rs505728	0.82[ASN][1000 genomes]
rs506081	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs509749	0.85[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs510143	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs512645	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs516509	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs516847	0.84[ASN][1000 genomes]
rs522897	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs539433	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs551827	0.85[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs551882	0.87[ASN][1000 genomes]
rs556810	0.86[CEU][hapmap];0.86[CHB][hapmap];1.00[JPT][hapmap];0.87[ASN][1000 genomes]
rs567306	0.82[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs569659	0.92[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.80[AMR][1000 genomes];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs569911	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs571841	0.86[CEU][hapmap];0.93[CHB][hapmap];1.00[JPT][hapmap];0.89[ASN][1000 genomes]
rs574610	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs576334	1.00[JPT][hapmap];0.85[ASN][1000 genomes]
rs577453	0.85[ASN][1000 genomes]
rs6427548	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs790625	0.85[ASN][1000 genomes]
rs790626	0.84[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs6667581	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs6667581	SLAMF7	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	chr1:160776000-160776600	ZNF genes & repeats	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:160776000-160776600	ZNF genes & repeats	Primary T helper cells fromperipheralblood	blood
21	chr1:160776000-160777200	ZNF genes & repeats	Primary T cells effector/memory enriched fromperipheralblood	blood
22	chr1:160776000-160777400	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:160776200-160777400	ZNF genes & repeats	Primary T killer naive cells fromperipheralblood	blood
24	chr1:160776200-160777800	ZNF genes & repeats	Primary Natural Killer cells fromperipheralblood	blood
25	chr1:160776400-160776800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood

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