Variant report

Variant	rs559644
Chromosome Location	chr11:64800438-64800439
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr11:64799194..64801472-chr11:64804094..64806308,2	MCF-7	breast:
2	chr11:64781097..64784077-chr11:64798309..64801053,4	MCF-7	breast:
3	chr11:64798286..64800870-chr11:64805869..64808336,2	K562	blood:
4	chr11:64798559..64800462-chr11:64801916..64804086,2	K562	blood:
5	chr11:64794902..64797457-chr11:64797903..64800553,2	MCF-7	breast:
6	chr11:64800138..64802225-chr11:64803720..64806117,3	K562	blood:

Variant related genes	Relation type
ENSG00000273003	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000110025	Chromatin interaction

Extended variants
information (count: 22 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs10897543	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11231929	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1196048	0.81[ASN][1000 genomes]
rs3862374	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs477539	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs484182	0.86[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs489489	0.81[ASN][1000 genomes]
rs496427	0.83[ASN][1000 genomes]
rs498636	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs532373	0.92[AFR][1000 genomes];0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs534236	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs548150	0.83[ASN][1000 genomes]
rs564966	0.81[ASN][1000 genomes]
rs598241	0.83[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs653111	0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs6591869	0.91[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 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
5	esv3369017	chr11:64800187-64800675	Strong transcription Weak transcription Transcr. at gene 5' and 3' Genic enhancers	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
6	esv3332812	chr11:64800207-64800645	Weak transcription Strong transcription	Chromatin interactive region	4 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs559644	SNX15	cis	Muscle Skeletal	GTEx

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64795200-64808000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr11:64795400-64808000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr11:64795600-64808000	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr11:64795800-64802400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
5	chr11:64795800-64805000	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr11:64795800-64807800	Weak transcription	HUES6 Cell Line	embryonic stem cell
7	chr11:64795800-64807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
8	chr11:64795800-64808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
9	chr11:64795800-64808000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr11:64796000-64800600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
11	chr11:64796000-64801400	Weak transcription	Aorta	Aorta
12	chr11:64796000-64803000	Weak transcription	HSMMtube	muscle
13	chr11:64796000-64805000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
14	chr11:64796000-64805000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
15	chr11:64796000-64807400	Weak transcription	Stomach Mucosa	stomach
16	chr11:64796000-64807600	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr11:64796000-64807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr11:64796000-64807800	Weak transcription	Fetal Kidney	kidney
19	chr11:64796000-64808000	Weak transcription	Pancreatic Islets	Pancreatic Islet
20	chr11:64796200-64801600	Weak transcription	Brain Substantia Nigra	brain
21	chr11:64796200-64802000	Weak transcription	Primary hematopoietic stem cells	blood
22	chr11:64796200-64803000	Weak transcription	NHLF	lung
23	chr11:64796200-64804200	Weak transcription	Fetal Heart	heart
24	chr11:64796200-64804400	Weak transcription	Muscle Satellite Cultured Cells	--
25	chr11:64796200-64805000	Weak transcription	NHDF-Ad	bronchial
26	chr11:64796200-64805600	Weak transcription	NH-A	brain
27	chr11:64796200-64807200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
28	chr11:64796200-64807200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
29	chr11:64796200-64807200	Weak transcription	K562	blood
30	chr11:64796200-64807800	Weak transcription	Small Intestine	intestine
31	chr11:64796200-64807800	Weak transcription	A549	lung
32	chr11:64796200-64807800	Weak transcription	HMEC	breast
33	chr11:64796200-64807800	Weak transcription	HUVEC	blood vessel
34	chr11:64796200-64807800	Weak transcription	NHEK	skin
35	chr11:64796200-64808000	Weak transcription	Osteobl	bone
36	chr11:64796400-64805400	Weak transcription	HSMM	muscle
37	chr11:64796400-64805800	Weak transcription	GM12878-XiMat	blood
38	chr11:64796400-64807400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
39	chr11:64796400-64807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
40	chr11:64796400-64807600	Weak transcription	Fetal Brain Male	brain
41	chr11:64796400-64807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
42	chr11:64796600-64807600	Strong transcription	Fetal Intestine Small	intestine
43	chr11:64796800-64806000	Strong transcription	Fetal Muscle Trunk	muscle
44	chr11:64796800-64807400	Strong transcription	Fetal Muscle Leg	muscle
45	chr11:64796800-64808000	Strong transcription	Fetal Stomach	stomach
46	chr11:64797000-64805000	Weak transcription	Psoas Muscle	Psoas
47	chr11:64798200-64806400	Strong transcription	Placenta	Placenta
48	chr11:64798400-64804200	Strong transcription	Stomach Smooth Muscle	stomach
49	chr11:64798400-64806200	Strong transcription	Monocytes-CD14+_RO01746	blood
50	chr11:64798400-64807400	Strong transcription	Skeletal Muscle Male	skeletal muscle

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