Variant report

Variant	rs477539
Chromosome Location	chr11:64820654-64820655
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64819293..64820855-chr11:64832360..64833915,2	K562	blood:
2	chr11:64807871..64811209-chr11:64819025..64821229,4	MCF-7	breast:
3	chr11:64819003..64820709-chr11:64820825..64822558,3	K562	blood:
4	chr11:64810649..64814377-chr11:64818779..64822031,5	K562	blood:
5	chr11:64808319..64812889-chr11:64818537..64822434,8	MCF-7	breast:
6	chr11:64820335..64821845-chr11:64827193..64829359,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000168061	Chromatin interaction
ENSG00000168060	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:30)

rs_ID	r²[population]
rs10897543	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11227118	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];0.92[JPT][hapmap];0.89[ASN][1000 genomes]
rs11231929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.93[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1196048	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.90[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1300845	0.85[JPT][hapmap]
rs2282498	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs2458298	0.84[CEU][hapmap]
rs36057475	0.89[ASN][1000 genomes]
rs3782094	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs3802936	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.93[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs484182	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.86[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs489489	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs496427	0.92[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs498636	0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs532373	0.96[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs534236	0.88[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs548150	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs559644	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs564966	0.96[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs566221	0.85[JPT][hapmap]
rs566908	1.00[YRI][hapmap]
rs598241	0.86[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs653111	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];0.87[AMR][1000 genomes];0.92[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs6591869	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.89[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];0.92[JPT][hapmap]
rs9971546	1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv526181	chr11:64638041-65257329	Flanking Active TSS Enhancers Strong transcription Active TSS Weak transcription Genic enhancers Transcr. at gene 5' and 3' 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	1539 gene(s)	inside rSNPs	diseases
2	nsv897709	chr11:64772545-64870779	Enhancers Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	64 gene(s)	inside rSNPs	diseases
3	nsv897710	chr11:64772545-64885445	Flanking Active TSS Strong transcription Genic enhancers Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	99 gene(s)	inside rSNPs	diseases
4	nsv897711	chr11:64772545-64900270	Genic enhancers Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	109 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs477539	SNX15	cis	Muscle Skeletal	GTEx

Chromatin state (count:31 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64813400-64821200	Weak transcription	Primary T cells from cord blood	blood
2	chr11:64813400-64824200	Weak transcription	HepG2	liver
3	chr11:64813800-64833200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
4	chr11:64814000-64827600	Weak transcription	Pancreas	Pancrea
5	chr11:64815800-64821000	Weak transcription	Fetal Thymus	thymus
6	chr11:64816000-64820800	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
7	chr11:64816000-64820800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
8	chr11:64816000-64821000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr11:64816000-64821000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
10	chr11:64816000-64821000	Weak transcription	Primary T helper cells PMA-I stimulated	--
11	chr11:64816000-64821000	Weak transcription	Fetal Intestine Large	intestine
12	chr11:64816000-64821000	Weak transcription	Fetal Intestine Small	intestine
13	chr11:64816000-64821000	Weak transcription	Monocytes-CD14+_RO01746	blood
14	chr11:64816000-64821200	Weak transcription	Primary neutrophils fromperipheralblood	blood
15	chr11:64816000-64821200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
16	chr11:64816000-64821200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
17	chr11:64816000-64821400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:64816200-64821000	Weak transcription	Primary B cells from peripheral blood	blood
19	chr11:64816200-64821000	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
20	chr11:64816200-64821000	Weak transcription	Primary T helper cells fromperipheralblood	blood
21	chr11:64816200-64821000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
22	chr11:64816200-64825800	Weak transcription	Rectal Mucosa Donor 29	rectum
23	chr11:64816400-64821400	Weak transcription	Spleen	Spleen
24	chr11:64820000-64821600	Enhancers	Esophagus	oesophagus
25	chr11:64820200-64821000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr11:64820200-64821200	ZNF genes & repeats	iPS DF 19.11 Cell Line	embryonic stem cell
27	chr11:64820200-64821200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr11:64820200-64822600	Enhancers	Primary hematopoietic stem cells	blood
29	chr11:64820400-64821200	Enhancers	GM12878-XiMat	blood
30	chr11:64820400-64822600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
31	chr11:64820600-64822400	Enhancers	Primary hematopoietic stem cells short term culture	blood

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