Variant report

Variant	rs3766374
Chromosome Location	chr1:160720554-160720555
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-SLAMF7-4	chr1:160720213-160722038	NONHSAT007075

Extended variants
information (count: 18 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs11265473	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11582702	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11588524	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1328111	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17313034	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs17313062	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2295616	0.91[EUR][1000 genomes]
rs35967351	0.91[EUR][1000 genomes]
rs3766370	0.80[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3766373	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs489286	0.85[EUR][1000 genomes]
rs495706	0.81[EUR][1000 genomes]
rs518242	0.82[AMR][1000 genomes]
rs518721	0.81[EUR][1000 genomes]
rs564883	0.85[AMR][1000 genomes];0.81[EUR][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	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	nsv428532	chr1:160671125-160767708	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3766374	SLAMF7	cis	multi-tissue	Pritchard
rs3766374	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs3766374	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:24 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160714400-160726800	Weak transcription	Primary B cells from peripheral blood	blood
2	chr1:160714800-160720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
3	chr1:160715200-160722800	Weak transcription	Colonic Mucosa	Colon
4	chr1:160715400-160720600	Weak transcription	Primary T helper cells PMA-I stimulated	--
5	chr1:160715400-160721200	Weak transcription	Primary T cells from cord blood	blood
6	chr1:160717000-160724400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr1:160717600-160723400	Enhancers	Primary T killer naive cells fromperipheralblood	blood
8	chr1:160718000-160721600	Genic enhancers	Primary T cells fromperipheralblood	blood
9	chr1:160718000-160723800	Genic enhancers	GM12878-XiMat	blood
10	chr1:160718400-160721400	Weak transcription	Pancreas	Pancrea
11	chr1:160718400-160726000	Enhancers	Primary T helper naive cells from peripheral blood	blood
12	chr1:160718400-160731000	Weak transcription	Esophagus	oesophagus
13	chr1:160719000-160722400	Weak transcription	Ovary	ovary
14	chr1:160719200-160722200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
15	chr1:160719400-160731200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
16	chr1:160719600-160721600	Weak transcription	NHEK	skin
17	chr1:160719800-160720600	Strong transcription	Duodenum Mucosa	Duodenum
18	chr1:160719800-160721000	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
19	chr1:160720000-160720800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
20	chr1:160720000-160720800	Genic enhancers	Spleen	Spleen
21	chr1:160720000-160723000	Enhancers	Fetal Thymus	thymus
22	chr1:160720200-160721800	Genic enhancers	Primary T killer memory cells from peripheral blood	blood
23	chr1:160720200-160723000	Enhancers	Thymus	Thymus
24	chr1:160720400-160721400	Strong transcription	Rectal Mucosa Donor 29	rectum

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