Variant report

Variant	rs562590
Chromosome Location	chr11:64803351-64803352
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:8)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:8 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64801971..64804817-chr11:64811001..64813793,2	K562	blood:
2	chr11:64798559..64800462-chr11:64801916..64804086,2	K562	blood:
3	chr11:64781092..64783206-chr11:64801514..64803932,2	K562	blood:
4	chr11:64793822..64797122-chr11:64800451..64804547,4	MCF-7	breast:
5	chr11:64800977..64804226-chr11:64805962..64809958,3	K562	blood:
6	chr11:64794559..64796593-chr11:64801577..64804441,3	K562	blood:
7	chr11:64793852..64797329-chr11:64802249..64805422,3	MCF-7	breast:
8	chr11:64794559..64796593-chr11:64801577..64803640,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000213465	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000270775	Chromatin interaction

Extended variants
information (count: 23 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10897544	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs1300845	1.00[ASW][hapmap];0.96[CEU][hapmap];0.94[CHB][hapmap];0.81[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.83[MKK][hapmap];0.97[TSI][hapmap];0.89[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2458298	0.94[ASW][hapmap];0.87[CEU][hapmap];0.93[GIH][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.94[TSI][hapmap];0.91[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2507814	1.00[CEU][hapmap];0.86[CHB][hapmap];0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs3741390	0.89[AMR][1000 genomes];0.86[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs3759041	0.96[CEU][hapmap];0.95[GIH][hapmap];0.94[MEX][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes]
rs3782094	0.84[CHB][hapmap]
rs3850947	0.98[GIH][hapmap];0.84[TSI][hapmap]
rs476824	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs486984	1.00[CEU][hapmap];0.89[CHB][hapmap];0.86[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs488686	0.96[CEU][hapmap];0.94[CHB][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs502333	0.94[ASW][hapmap];1.00[CEU][hapmap];0.89[CHB][hapmap];0.87[CHD][hapmap];0.95[GIH][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.96[MKK][hapmap];0.91[TSI][hapmap];0.96[YRI][hapmap];0.94[AFR][1000 genomes];0.91[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs525433	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs533018	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs566221	0.96[CEU][hapmap];0.94[CHB][hapmap];0.85[CHD][hapmap];0.98[GIH][hapmap];0.94[MEX][hapmap];0.82[MKK][hapmap];0.97[TSI][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs613874	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs620981	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs678614	0.99[AFR][1000 genomes];0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs947799	0.84[CHB][hapmap]

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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs562590	SNX15	cis	lymphoblastoid	seeQTL
rs562590	SNX15	cis	parietal	SCAN
rs562590	RAB1B	cis	parietal	SCAN
rs562590	B3GAT3	cis	cerebellum	SCAN
rs562590	SNX15	cis	Muscle Skeletal	GTEx
rs562590	MARK2	cis	cerebellum	SCAN
rs562590	SPDYC	cis	parietal	SCAN
rs562590	LRRN4CL	cis	parietal	SCAN
rs562590	SCGB2A2	cis	cerebellum	SCAN

Chromatin state (count:122 , 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	chr11:64795800-64805000	Weak transcription	HUES48 Cell Line	embryonic stem cell
5	chr11:64795800-64807800	Weak transcription	HUES6 Cell Line	embryonic stem cell
6	chr11:64795800-64807800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr11:64795800-64808000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
8	chr11:64795800-64808000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
9	chr11:64796000-64805000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
10	chr11:64796000-64805000	Weak transcription	iPS-20b Cell Line	embryonic stem cell
11	chr11:64796000-64807400	Weak transcription	Stomach Mucosa	stomach
12	chr11:64796000-64807600	Weak transcription	H1 Cell Line	embryonic stem cell
13	chr11:64796000-64807800	Weak transcription	HUES64 Cell Line	embryonic stem cell
14	chr11:64796000-64807800	Weak transcription	Fetal Kidney	kidney
15	chr11:64796000-64808000	Weak transcription	Pancreatic Islets	Pancreatic Islet
16	chr11:64796200-64804200	Weak transcription	Fetal Heart	heart
17	chr11:64796200-64804400	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr11:64796200-64805000	Weak transcription	NHDF-Ad	bronchial
19	chr11:64796200-64805600	Weak transcription	NH-A	brain
20	chr11:64796200-64807200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr11:64796200-64807200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
22	chr11:64796200-64807200	Weak transcription	K562	blood
23	chr11:64796200-64807800	Weak transcription	Small Intestine	intestine
24	chr11:64796200-64807800	Weak transcription	A549	lung
25	chr11:64796200-64807800	Weak transcription	HMEC	breast
26	chr11:64796200-64807800	Weak transcription	HUVEC	blood vessel
27	chr11:64796200-64807800	Weak transcription	NHEK	skin
28	chr11:64796200-64808000	Weak transcription	Osteobl	bone
29	chr11:64796400-64805400	Weak transcription	HSMM	muscle
30	chr11:64796400-64805800	Weak transcription	GM12878-XiMat	blood
31	chr11:64796400-64807400	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
32	chr11:64796400-64807400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
33	chr11:64796400-64807600	Weak transcription	Fetal Brain Male	brain
34	chr11:64796400-64807800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
35	chr11:64796600-64807600	Strong transcription	Fetal Intestine Small	intestine
36	chr11:64796800-64806000	Strong transcription	Fetal Muscle Trunk	muscle
37	chr11:64796800-64807400	Strong transcription	Fetal Muscle Leg	muscle
38	chr11:64796800-64808000	Strong transcription	Fetal Stomach	stomach
39	chr11:64797000-64805000	Weak transcription	Psoas Muscle	Psoas
40	chr11:64798200-64806400	Strong transcription	Placenta	Placenta
41	chr11:64798400-64804200	Strong transcription	Stomach Smooth Muscle	stomach
42	chr11:64798400-64806200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr11:64798400-64807400	Strong transcription	Skeletal Muscle Male	skeletal muscle
44	chr11:64798400-64807800	Strong transcription	Fetal Intestine Large	intestine
45	chr11:64798400-64807800	Strong transcription	Sigmoid Colon	Sigmoid Colon
46	chr11:64798600-64804000	Strong transcription	Brain Cingulate Gyrus	brain
47	chr11:64798600-64807200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
48	chr11:64798600-64807600	Strong transcription	Brain Germinal Matrix	brain
49	chr11:64798600-64807600	Strong transcription	Brain Inferior Temporal Lobe	brain
50	chr11:64798600-64807800	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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