Variant report

Variant	rs2272343
Chromosome Location	chr7:99778285-99778286
allele	A/C
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	ELF1	chr7:99778010-99778520	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr7:99754180..99757947-chr7:99773944..99778293,5	K562	blood:
2	chr7:99751463..99761050-chr7:99772463..99778676,10	K562	blood:

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-C7orf59-1	chr7:99778116-99778518	NONHSAT122344

Variant related genes	Relation type
STAG3	TF binding region
GPC2	TF binding region
ENSG00000266154	Chromatin interaction
ENSG00000146826	Chromatin interaction

Extended variants
information (count: 27 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10246243	0.96[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10269641	0.87[EUR][1000 genomes]
rs11531577	0.84[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11762932	1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11771660	0.87[EUR][1000 genomes]
rs12056000	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2056726	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs55839153	0.82[EUR][1000 genomes]
rs56089143	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs59248100	0.86[EUR][1000 genomes]
rs6943160	0.83[EUR][1000 genomes]
rs6947033	0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6953580	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs73399514	0.95[EUR][1000 genomes]
rs7782305	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7786505	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7789890	0.89[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs7801070	0.90[EUR][1000 genomes]
rs941288	0.84[EUR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:8 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv534298	chr7:99478011-99886076	Flanking Active TSS Enhancers Genic enhancers Strong transcription Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1132 gene(s)	inside rSNPs	diseases
2	nsv607931	chr7:99664817-99796146	Bivalent Enhancer Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Active TSS Weak transcription Strong transcription Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1097 gene(s)	inside rSNPs	diseases
3	esv1798486	chr7:99689883-99930879	Active TSS Weak transcription Flanking Active TSS Enhancers Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
4	esv1833059	chr7:99689883-99930879	Flanking Active TSS Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1085 gene(s)	inside rSNPs	diseases
5	esv3350965	chr7:99747460-100146105	Weak transcription Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	304 gene(s)	inside rSNPs	diseases
6	nsv427794	chr7:99750981-99960900	Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
7	nsv428180	chr7:99750981-99960900	Weak transcription Enhancers Bivalent/Poised TSS Active TSS Strong transcription Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
8	nsv5867	chr7:99766774-99799755	Active TSS Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	20 gene(s)	inside rSNPs	diseases

mRNA abundance (count:9)

SNP	Gene	Cis/trans	Tissue	Source
rs2272343	PILRB	cis	lung	GTEx
rs2272343	STAG3L5P	cis	Nerve Tibial	GTEx
rs2272343	LOC389541	Cis_1M	lymphoblastoid	RTeQTL
rs2272343	PVRIG	Cis_1M	lymphoblastoid	RTeQTL
rs2272343	STAG3	Cis_1M	lymphoblastoid	RTeQTL
rs2272343	PILRA	cis	Thyroid	GTEx
rs2272343	PILRB	Cis_1M	lymphoblastoid	RTeQTL
rs2272343	PILRB	cis	Nerve Tibial	GTEx
rs2272343	PILRB	cis	Artery Tibial	GTEx

Chromatin state (count:23 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr7:99775000-99780600	Enhancers	Primary T cells from cord blood	blood
2	chr7:99775800-99779400	Enhancers	Primary T cells fromperipheralblood	blood
3	chr7:99775800-99787600	Weak transcription	GM12878-XiMat	blood
4	chr7:99775800-99798000	Weak transcription	Breast Myoepithelial Primary Cells	Breast
5	chr7:99776000-99780400	Enhancers	Fetal Thymus	thymus
6	chr7:99776400-99778600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
7	chr7:99777600-99778800	Enhancers	Thymus	Thymus
8	chr7:99777800-99778800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
9	chr7:99777800-99779400	Enhancers	Primary T helper naive cells fromperipheralblood	blood
10	chr7:99777800-99779600	Enhancers	Primary T helper cells fromperipheralblood	blood
11	chr7:99778000-99778600	Enhancers	Primary hematopoietic stem cells short term culture	blood
12	chr7:99778000-99778800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
13	chr7:99778000-99778800	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
14	chr7:99778000-99778800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
15	chr7:99778000-99779000	Enhancers	Primary T helper cells PMA-I stimulated	--
16	chr7:99778000-99779200	Enhancers	Primary T killer memory cells from peripheral blood	blood
17	chr7:99778000-99779400	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
18	chr7:99778000-99779400	Enhancers	Primary T helper naive cells from peripheral blood	blood
19	chr7:99778200-99778400	Flanking Active TSS	Dnd41	blood
20	chr7:99778200-99778400	Enhancers	K562	blood
21	chr7:99778200-99778600	Enhancers	Primary B cells from peripheral blood	blood
22	chr7:99778200-99778800	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
23	chr7:99778200-99779800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell

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