Variant report

Variant	rs17313062
Chromosome Location	chr1:160717741-160717742
allele	A/G
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	STAT3	chr1:160717610-160717751	MCF10A-Er-Src	breast:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr1:160714727..160717750-chr1:160718869..160722108,3	K562	blood:
2	chr1:160716030..160718283-chr1:161088613..161090888,2	K562	blood:

Variant related genes	Relation type
SLAMF7	TF binding region
ENSG00000158793	Chromatin interaction
ENSG00000026751	Chromatin interaction

Extended variants
information (count: 19 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:16)

rs_ID	r²[population]
rs11265473	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11582702	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11588524	0.89[AFR][1000 genomes];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs1328111	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs17313034	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2176873	0.80[AMR][1000 genomes]
rs2295616	0.91[EUR][1000 genomes]
rs35967351	0.91[EUR][1000 genomes]
rs3766370	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs3766373	0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs3766374	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs489286	0.85[EUR][1000 genomes]
rs495706	0.81[EUR][1000 genomes]
rs518242	0.84[AMR][1000 genomes]
rs518721	0.81[EUR][1000 genomes]
rs564883	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
rs17313062	LY9	Cis_1M	lymphoblastoid	RTeQTL
rs17313062	SLAMF7	Cis_1M	lymphoblastoid	RTeQTL
rs17313062	SLAMF7	cis	multi-tissue	Pritchard

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr1:160709400-160718400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
2	chr1:160712800-160718000	Enhancers	Primary T cells fromperipheralblood	blood
3	chr1:160713000-160720400	Weak transcription	Rectal Mucosa Donor 29	rectum
4	chr1:160713600-160718200	Weak transcription	Spleen	Spleen
5	chr1:160714400-160718200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
6	chr1:160714400-160719800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr1:160714400-160726800	Weak transcription	Primary B cells from peripheral blood	blood
8	chr1:160714800-160720800	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr1:160715200-160717800	Weak transcription	Primary monocytes fromperipheralblood	blood
10	chr1:160715200-160717800	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr1:160715200-160719800	Weak transcription	Duodenum Mucosa	Duodenum
12	chr1:160715200-160720000	Weak transcription	Fetal Thymus	thymus
13	chr1:160715200-160720200	Weak transcription	Thymus	Thymus
14	chr1:160715200-160722800	Weak transcription	Colonic Mucosa	Colon
15	chr1:160715400-160719600	Weak transcription	Primary T helper cells fromperipheralblood	blood
16	chr1:160715400-160720600	Weak transcription	Primary T helper cells PMA-I stimulated	--
17	chr1:160715400-160721200	Weak transcription	Primary T cells from cord blood	blood
18	chr1:160715600-160718000	Enhancers	ES-I3 Cell Line	embryonic stem cell
19	chr1:160716200-160717800	Enhancers	iPS-15b Cell Line	embryonic stem cell
20	chr1:160717000-160724400	Genic enhancers	Primary Natural Killer cells fromperipheralblood	blood
21	chr1:160717200-160719400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
22	chr1:160717400-160718200	Weak transcription	Ovary	ovary
23	chr1:160717400-160718200	Enhancers	A549	lung
24	chr1:160717600-160717800	Genic enhancers	GM12878-XiMat	blood
25	chr1:160717600-160718000	Weak transcription	Sigmoid Colon	Sigmoid Colon
26	chr1:160717600-160718400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
27	chr1:160717600-160718400	Enhancers	NHEK	skin
28	chr1:160717600-160719200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
29	chr1:160717600-160720200	Enhancers	Primary T killer memory cells from peripheral blood	blood
30	chr1:160717600-160723400	Enhancers	Primary T killer naive cells fromperipheralblood	blood

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