Variant report

Variant	rs539433
Chromosome Location	chr1:160789421-160789422
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160786153..160788877-chr1:160788974..160791369,2	K562	blood:
2	chr1:160787480..160789463-chr1:161085547..161088382,2	K562	blood:

Variant related genes	Relation type
ENSG00000143256	Chromatin interaction
ENSG00000158793	Chromatin interaction

Extended variants
information (count: 37 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:34)

rs_ID	r²[population]
rs11265487	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11265488	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11265489	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2027015	0.81[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2779800	0.97[ASN][1000 genomes]
rs474131	0.97[ASN][1000 genomes]
rs485618	0.92[ASN][1000 genomes]
rs492874	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs492906	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];0.88[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs494091	0.88[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs496201	0.88[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs504848	0.95[ASN][1000 genomes]
rs505728	0.91[ASN][1000 genomes]
rs506081	0.97[ASN][1000 genomes]
rs509749	0.97[ASN][1000 genomes]
rs510143	0.97[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs512645	0.94[ASN][1000 genomes]
rs516509	0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs516847	0.92[ASN][1000 genomes]
rs522897	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs551827	0.97[ASN][1000 genomes]
rs551882	0.96[ASN][1000 genomes]
rs556810	0.96[ASN][1000 genomes]
rs567306	0.86[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs569659	0.92[AFR][1000 genomes];0.94[AMR][1000 genomes];0.89[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs569911	0.94[ASN][1000 genomes]
rs571841	0.90[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs574610	0.94[ASN][1000 genomes]
rs576334	0.94[ASN][1000 genomes]
rs577453	0.94[ASN][1000 genomes]
rs6427548	0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6667581	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs790625	0.92[ASN][1000 genomes]
rs790626	0.92[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
rs539433	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs539433	LY9	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 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	chr1:160778000-160795600	Weak transcription	Sigmoid Colon	Sigmoid Colon
3	chr1:160778000-160798400	Strong transcription	Primary B cells from peripheral blood	blood
4	chr1:160778400-160799600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
5	chr1:160780000-160789800	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
6	chr1:160782400-160798200	Strong transcription	Primary T helper cells PMA-I stimulated	--
7	chr1:160782600-160803200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
8	chr1:160782800-160789600	Strong transcription	Primary T helper naive cells fromperipheralblood	blood
9	chr1:160783400-160791000	Weak transcription	Duodenum Mucosa	Duodenum
10	chr1:160783600-160790000	Strong transcription	Primary T helper memory cells from peripheral blood 2	blood
11	chr1:160783800-160798200	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr1:160783800-160801000	Strong transcription	Primary T helper cells fromperipheralblood	blood
13	chr1:160783800-160803200	Strong transcription	Primary T cells fromperipheralblood	blood
14	chr1:160786600-160792800	Weak transcription	Spleen	Spleen
15	chr1:160788200-160793200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr1:160789000-160790000	Weak transcription	Primary B cells from cord blood	blood
17	chr1:160789000-160791200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
18	chr1:160789200-160790600	Weak transcription	Primary T cells from cord blood	blood
19	chr1:160789200-160791200	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
20	chr1:160789200-160792000	Weak transcription	Thymus	Thymus
21	chr1:160789200-160792400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr1:160789400-160792400	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
23	chr1:160789400-160792600	Weak transcription	Primary T killer memory cells from peripheral blood	blood
24	chr1:160789400-160792800	Weak transcription	Fetal Thymus	thymus

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