Variant report

Variant	rs11231929
Chromosome Location	chr11:64810771-64810772
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:16)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:16 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64793282..64795774-chr11:64807101..64811680,5	K562	blood:
2	chr11:64793697..64796700-chr11:64806482..64812345,9	MCF-7	breast:
3	chr11:64807050..64811411-chr11:64876533..64881108,6	MCF-7	breast:
4	chr11:64810091..64812972-chr11:64883728..64886202,2	MCF-7	breast:
5	chr11:64803567..64805727-chr11:64810246..64813138,2	K562	blood:
6	chr11:64807684..64812709-chr11:64850593..64853492,4	MCF-7	breast:
7	chr11:64807810..64812277-chr11:64813364..64817609,8	MCF-7	breast:
8	chr11:64805658..64811611-chr11:64862545..64865451,9	MCF-7	breast:
9	chr11:64809180..64811372-chr11:64815514..64817240,2	K562	blood:
10	chr11:64808483..64810483-chr11:64810664..64814353,4	K562	blood:
11	chr11:64804480..64810811-chr11:64850224..64856247,12	K562	blood:
12	chr11:64808732..64812218-chr11:64877838..64879922,3	MCF-7	breast:
13	chr11:64794773..64796855-chr11:64809238..64812332,3	K562	blood:
14	chr11:64810755..64812822-chr11:64850168..64852033,2	MCF-7	breast:
15	chr11:64806644..64812839-chr11:64862132..64865938,9	MCF-7	breast:
16	chr11:64682450..64685608-chr11:64808232..64811277,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000162300	Chromatin interaction
ENSG00000149823	Chromatin interaction
ENSG00000255173	Chromatin interaction
ENSG00000174276	Chromatin interaction
ENSG00000168061	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000068971	Chromatin interaction
ENSG00000146670	Chromatin interaction
ENSG00000168060	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000254501	Chromatin interaction
ENSG00000110046	Chromatin interaction
ENSG00000266123	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 7 )

rSNPs within LD-proxies of this variant (count:31)

rs_ID	r²[population]
rs10897543	0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11227118	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];0.92[JPT][hapmap];0.83[ASN][1000 genomes]
rs1196048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1300845	0.85[JPT][hapmap]
rs2282498	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs2458298	0.81[CEU][hapmap]
rs36057475	0.83[ASN][1000 genomes]
rs3782094	0.82[CHB][hapmap];0.92[JPT][hapmap]
rs3802936	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.81[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	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]
rs477539	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]
rs484182	0.96[CEU][hapmap];0.94[CHB][hapmap];0.92[JPT][hapmap];0.91[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs488686	0.85[JPT][hapmap]
rs489489	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs496427	0.86[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs498636	0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs532373	0.96[CEU][hapmap];0.92[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];0.92[JPT][hapmap];0.87[TSI][hapmap];0.92[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs548150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.97[TSI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs559644	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs564966	1.00[CEU][hapmap];1.00[CHB][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.86[AMR][1000 genomes];0.84[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs566221	0.85[JPT][hapmap]
rs566908	0.86[ASW][hapmap];1.00[YRI][hapmap]
rs598241	0.90[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];0.92[JPT][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.91[AMR][1000 genomes];0.96[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];0.92[JPT][hapmap];0.84[MEX][hapmap];0.90[TSI][hapmap];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][hapmap];0.83[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];0.95[GIH][hapmap];0.92[JPT][hapmap];0.90[MEX][hapmap];0.87[TSI][hapmap]
rs9971546	1.00[CHB][hapmap];0.89[CHD][hapmap];0.92[JPT][hapmap];1.00[YRI][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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs11231929	SUV420H1	cis	parietal	SCAN
rs11231929	SNX15	cis	parietal	SCAN
rs11231929	SPDYC	cis	parietal	SCAN
rs11231929	SNX15	cis	Muscle Skeletal	GTEx
rs11231929	RPS6KA4	cis	lymphoblastoid	GTEx
rs11231929	SCGB2A2	cis	cerebellum	SCAN
rs11231929	SNX15	cis	lymphoblastoid	seeQTL

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64808000-64810800	Active TSS	NHLF	lung
2	chr11:64809000-64812000	Enhancers	Placenta	Placenta
3	chr11:64809400-64811400	Weak transcription	Gastric	stomach
4	chr11:64809600-64810800	Enhancers	Breast Myoepithelial Primary Cells	Breast
5	chr11:64809600-64811000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
6	chr11:64809600-64811200	Weak transcription	Right Atrium	heart
7	chr11:64809600-64811200	Enhancers	Skeletal Muscle Female	skeletal muscle
8	chr11:64809600-64811200	Enhancers	Monocytes-CD14+_RO01746	blood
9	chr11:64809600-64811400	Weak transcription	Primary hematopoietic stem cells	blood
10	chr11:64809600-64811400	Weak transcription	Brain Cingulate Gyrus	brain
11	chr11:64809600-64811400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr11:64809600-64811400	Weak transcription	Colonic Mucosa	Colon
13	chr11:64809600-64811400	Enhancers	Rectal Mucosa Donor 31	rectum
14	chr11:64809600-64811400	Weak transcription	Right Ventricle	heart
15	chr11:64809600-64811600	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr11:64809600-64811600	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
17	chr11:64809600-64811600	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr11:64809600-64811600	Weak transcription	Brain Angular Gyrus	brain
19	chr11:64809600-64811600	Weak transcription	Duodenum Smooth Muscle	Duodenum
20	chr11:64809600-64811600	Weak transcription	Rectal Smooth Muscle	rectum
21	chr11:64809600-64811800	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr11:64809600-64811800	Weak transcription	Primary T cells from cord blood	blood
23	chr11:64809600-64811800	Enhancers	Adipose Nuclei	Adipose
24	chr11:64809600-64811800	Weak transcription	Aorta	Aorta
25	chr11:64809600-64812000	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
26	chr11:64809600-64812000	Weak transcription	Brain Substantia Nigra	brain
27	chr11:64809600-64812000	Enhancers	Rectal Mucosa Donor 29	rectum
28	chr11:64809600-64812400	Enhancers	Primary monocytes fromperipheralblood	blood
29	chr11:64809600-64812400	Weak transcription	Left Ventricle	heart
30	chr11:64809600-64814800	Weak transcription	Stomach Mucosa	stomach
31	chr11:64809800-64810800	Enhancers	Fetal Intestine Large	intestine
32	chr11:64809800-64810800	Transcr. at gene 5' and 3'	Dnd41	blood
33	chr11:64809800-64811400	Enhancers	NHDF-Ad	bronchial
34	chr11:64809800-64811600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
35	chr11:64809800-64811800	Flanking Active TSS	Hela-S3	cervix
36	chr11:64809800-64814600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
37	chr11:64809800-64814600	Weak transcription	Primary B cells from cord blood	blood
38	chr11:64809800-64814600	Genic enhancers	Fetal Muscle Trunk	muscle
39	chr11:64809800-64814800	Weak transcription	NH-A	brain
40	chr11:64810000-64810800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
41	chr11:64810000-64810800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
42	chr11:64810000-64811200	Weak transcription	Stomach Smooth Muscle	stomach
43	chr11:64810000-64811200	Enhancers	K562	blood
44	chr11:64810000-64811600	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
45	chr11:64810000-64811600	Enhancers	Duodenum Mucosa	Duodenum
46	chr11:64810000-64812200	Weak transcription	Liver	Liver
47	chr11:64810000-64812800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
48	chr11:64810000-64814200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
49	chr11:64810000-64814200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
50	chr11:64810000-64814400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood

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