Variant report

Variant	rs11658582
Chromosome Location	chr17:38763200-38763201
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr17:38751255..38752916-chr17:38763179..38764693,2	MCF-7	breast:
2	chr17:38755696..38758368-chr17:38761351..38764585,4	K562	blood:
3	chr17:38735976..38740811-chr17:38759775..38765396,5	MCF-7	breast:
4	chr17:38761736..38765184-chr17:39682897..39687464,6	MCF-7	breast:
5	chr17:38718371..38719906-chr17:38760892..38763624,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000171345	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:23)

rs_ID	r²[population]
rs1013971	0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1048572	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs1048573	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs2014704	0.89[JPT][hapmap]
rs3752026	0.88[CHB][hapmap];1.00[JPT][hapmap]
rs4890093	0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs4890117	0.84[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6503549	0.83[JPT][hapmap]
rs7209467	0.89[JPT][hapmap]
rs7209735	0.87[JPT][hapmap]
rs7221109	0.88[AFR][1000 genomes];0.95[AMR][1000 genomes];0.90[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7223136	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7223332	0.81[JPT][hapmap]
rs7226035	0.83[AMR][1000 genomes];0.81[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs757411	0.92[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.89[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs8068721	0.82[JPT][hapmap]
rs8076587	0.84[JPT][hapmap]
rs917593	0.82[JPT][hapmap]
rs917595	0.84[JPT][hapmap]
rs9896791	0.82[JPT][hapmap]
rs9906785	0.94[ASN][1000 genomes]
rs9911533	0.90[AMR][1000 genomes];0.85[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs9915135	0.94[CHB][hapmap];1.00[JPT][hapmap];0.94[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	nsv574994	chr17:38719799-38824636	Enhancers Flanking Active TSS Strong transcription Weak transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
2	esv2758454	chr17:38748300-38850104	Active TSS Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases
3	esv2758689	chr17:38748300-38850104	Weak transcription Genic enhancers Enhancers Strong transcription Flanking Active TSS Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11658582	CCR7	Cis_1M	lymphoblastoid	RTeQTL
rs11658582	SMARCE1	Cis_1M	lymphoblastoid	RTeQTL
rs11658582	SMARCE1	cis	multi-tissue	Pritchard

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr17:38755200-38763600	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
2	chr17:38755400-38763800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
3	chr17:38755800-38764400	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
4	chr17:38757200-38763600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr17:38758200-38765200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
6	chr17:38759000-38765400	Enhancers	Placenta	Placenta
7	chr17:38759600-38763200	Weak transcription	Placenta Amnion	Placenta Amnion
8	chr17:38759600-38763400	Enhancers	Primary T helper cells fromperipheralblood	blood
9	chr17:38759600-38763800	Weak transcription	Primary B cells from peripheral blood	blood
10	chr17:38759800-38763200	Weak transcription	Fetal Stomach	stomach
11	chr17:38759800-38763800	Weak transcription	Primary B cells from cord blood	blood
12	chr17:38759800-38764200	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
13	chr17:38760800-38766200	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
14	chr17:38761200-38765000	Weak transcription	Adipose Nuclei	Adipose
15	chr17:38761600-38764000	Enhancers	Primary T cells fromperipheralblood	blood
16	chr17:38761800-38764000	Enhancers	Primary T cells from cord blood	blood
17	chr17:38761800-38769000	Weak transcription	Esophagus	oesophagus
18	chr17:38761800-38769000	Weak transcription	Spleen	Spleen
19	chr17:38762000-38763800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
20	chr17:38762000-38763800	Enhancers	Primary T regulatory cells fromperipheralblood	blood
21	chr17:38762000-38763800	Enhancers	Primary T killer naive cells fromperipheralblood	blood
22	chr17:38762200-38763400	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr17:38762200-38763400	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr17:38762200-38765400	Enhancers	Fetal Thymus	thymus
25	chr17:38762600-38763200	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
26	chr17:38762600-38763200	Weak transcription	Lung	lung
27	chr17:38762600-38763400	Enhancers	Primary T killer memory cells from peripheral blood	blood
28	chr17:38762600-38763400	Enhancers	Sigmoid Colon	Sigmoid Colon
29	chr17:38763000-38764800	Enhancers	HUES6 Cell Line	embryonic stem cell
30	chr17:38763200-38763600	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr17:38763200-38763800	Enhancers	Fetal Stomach	stomach
32	chr17:38763200-38764200	Enhancers	Lung	lung
33	chr17:38763200-38764600	Flanking Active TSS	Primary T helper 17 cells PMA-I stimulated	--
34	chr17:38763200-38764600	Enhancers	Placenta Amnion	Placenta Amnion

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