Variant report

Variant	rs3862374
Chromosome Location	chr11:64809441-64809442
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:27)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:27 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64806669..64810557-chr11:64862016..64868359,8	K562	blood:
2	chr11:64793282..64795774-chr11:64807101..64811680,5	K562	blood:
3	chr11:64793697..64796700-chr11:64806482..64812345,9	MCF-7	breast:
4	chr11:64780179..64786029-chr11:64807067..64810211,7	MCF-7	breast:
5	chr11:64787088..64789367-chr11:64807052..64810027,2	MCF-7	breast:
6	chr11:64807090..64809871-chr11:64850334..64853304,4	MCF-7	breast:
7	chr11:64780338..64782626-chr11:64806994..64809935,3	K562	blood:
8	chr11:64807050..64811411-chr11:64876533..64881108,6	MCF-7	breast:
9	chr11:64644663..64647408-chr11:64807363..64809566,4	MCF-7	breast:
10	chr11:64808477..64810468-chr11:64816977..64818703,3	MCF-7	breast:
11	chr11:64807534..64810713-chr11:64846257..64849828,3	MCF-7	breast:
12	chr11:64808945..64810714-chr11:64850630..64853153,2	K562	blood:
13	chr11:64806772..64810496-chr11:64862454..64866792,5	K562	blood:
14	chr11:64807959..64809979-chr11:64878035..64880846,2	K562	blood:
15	chr11:64808323..64810154-chr11:64871056..64873673,2	MCF-7	breast:
16	chr11:64793793..64795353-chr11:64806843..64809654,4	MCF-7	breast:
17	chr11:64807684..64812709-chr11:64850593..64853492,4	MCF-7	breast:
18	chr11:64808483..64810483-chr11:64810664..64814353,4	K562	blood:
19	chr11:64807810..64812277-chr11:64813364..64817609,8	MCF-7	breast:
20	chr11:64805658..64811611-chr11:64862545..64865451,9	MCF-7	breast:
21	chr11:64809180..64811372-chr11:64815514..64817240,2	K562	blood:
22	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
23	chr11:64808732..64812218-chr11:64877838..64879922,3	MCF-7	breast:
24	chr11:64794773..64796855-chr11:64809238..64812332,3	K562	blood:
25	chr11:64806644..64812839-chr11:64862132..64865938,9	MCF-7	breast:
26	chr11:64682450..64685608-chr11:64808232..64811277,3	MCF-7	breast:
27	chr11:64807549..64809979-chr11:64878035..64880006,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000254501	Chromatin interaction
ENSG00000266123	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000110046	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000110047	Chromatin interaction
ENSG00000162300	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000149823	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs10897543	0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227118	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs11231929	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];0.92[JPT][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1196048	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2282498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs2458298	0.81[CEU][hapmap]
rs2507814	0.83[JPT][hapmap]
rs36057475	0.83[ASN][1000 genomes]
rs3782094	0.82[CHB][hapmap];1.00[JPT][hapmap]
rs3802936	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs477539	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];1.00[JPT][hapmap];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs486984	0.82[JPT][hapmap]
rs489489	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs496427	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs498636	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs532373	0.96[CEU][hapmap];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs534236	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.93[GIH][hapmap];1.00[JPT][hapmap];0.88[MKK][hapmap];0.92[TSI][hapmap];0.81[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs548150	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.92[TSI][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559644	0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs598241	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs653111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];1.00[TSI][hapmap];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs6591869	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.85[MEX][hapmap];0.95[TSI][hapmap];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.83[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.90[MEX][hapmap];0.81[TSI][hapmap]
rs9971546	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 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	esv3324692	chr11:64806676-64811174	Weak transcription Genic enhancers Active TSS Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region	22 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs3862374	SUV420H1	cis	parietal	SCAN
rs3862374	SPDYC	cis	parietal	SCAN
rs3862374	SNX15	cis	Muscle Skeletal	GTEx
rs3862374	SNX15	cis	lymphoblastoid	seeQTL
rs3862374	SNX15	cis	parietal	SCAN
rs3862374	RAB1B	cis	parietal	SCAN
rs3862374	RPS6KA4	cis	lymphoblastoid	GTEx
rs3862374	SCGB2A2	cis	cerebellum	SCAN

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64807800-64809600	Active TSS	ES-WA7 Cell Line	embryonic stem cell
2	chr11:64807800-64809800	Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
3	chr11:64807800-64810000	Active TSS	ES-I3 Cell Line	embryonic stem cell
4	chr11:64807800-64810000	Active TSS	iPS-18 Cell Line	embryonic stem cell
5	chr11:64807800-64810400	Active TSS	iPS-20b Cell Line	embryonic stem cell
6	chr11:64807800-64810600	Active TSS	HUES64 Cell Line	embryonic stem cell
7	chr11:64808000-64809600	Active TSS	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
8	chr11:64808000-64809600	Active TSS	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr11:64808000-64809600	Active TSS	ES-UCSF4 Cell Line	embryonic stem cell
10	chr11:64808000-64809600	Active TSS	Brain Cingulate Gyrus	brain
11	chr11:64808000-64809600	Active TSS	Fetal Kidney	kidney
12	chr11:64808000-64809600	Active TSS	Pancreatic Islets	Pancreatic Islet
13	chr11:64808000-64809600	Active TSS	Ovary	ovary
14	chr11:64808000-64809600	Active TSS	Rectal Smooth Muscle	rectum
15	chr11:64808000-64809800	Active TSS	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
16	chr11:64808000-64809800	Active TSS	Fetal Brain Female	brain
17	chr11:64808000-64809800	Active TSS	A549	lung
18	chr11:64808000-64809800	Active TSS	NHDF-Ad	bronchial
19	chr11:64808000-64810000	Active TSS	H1 Cell Line	embryonic stem cell
20	chr11:64808000-64810000	Active TSS	iPS-15b Cell Line	embryonic stem cell
21	chr11:64808000-64810000	Active TSS	HepG2	liver
22	chr11:64808000-64810200	Active TSS	H9 Cell Line	embryonic stem cell
23	chr11:64808000-64810200	Active TSS	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
24	chr11:64808000-64810200	Active TSS	HUES48 Cell Line	embryonic stem cell
25	chr11:64808000-64810200	Active TSS	HUES6 Cell Line	embryonic stem cell
26	chr11:64808000-64810200	Active TSS	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
27	chr11:64808000-64810200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
28	chr11:64808000-64810800	Active TSS	NHLF	lung
29	chr11:64808200-64809600	Active TSS	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr11:64808200-64809600	Active TSS	Aorta	Aorta
31	chr11:64808200-64809600	Active TSS	Brain Angular Gyrus	brain
32	chr11:64808200-64809600	Active TSS	Brain Hippocampus Middle	brain
33	chr11:64808200-64809600	Active TSS	Colon Smooth Muscle	Colon
34	chr11:64808200-64809600	Active TSS	Stomach Mucosa	stomach
35	chr11:64808200-64809600	Active TSS	HSMMtube	muscle
36	chr11:64808200-64809800	Active TSS	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr11:64808200-64809800	Active TSS	GM12878-XiMat	blood
38	chr11:64808200-64809800	Active TSS	Hela-S3	cervix
39	chr11:64808200-64810000	Active TSS	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr11:64808200-64810000	Active TSS	H9 Derived Neuron Cultured Cells	ES cell derived
41	chr11:64808200-64810000	Active TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
42	chr11:64808200-64810000	Active TSS	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
43	chr11:64808200-64810200	Active TSS	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr11:64808200-64810400	Active TSS	HSMM	muscle
45	chr11:64808400-64809600	Active TSS	Duodenum Smooth Muscle	Duodenum
46	chr11:64808400-64809800	Active TSS	Dnd41	blood
47	chr11:64808400-64809800	Active TSS	NH-A	brain
48	chr11:64808400-64810000	Active TSS	Muscle Satellite Cultured Cells	--
49	chr11:64808400-64810000	Active TSS	HMEC	breast
50	chr11:64808800-64809600	Flanking Active TSS	Primary B cells from cord blood	blood

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