Variant report

Variant	rs489489
Chromosome Location	chr11:64845438-64845439
allele	A/C
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:17)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:17 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr11:64835460..64837295-chr11:64843950..64846187,2	K562	blood:
2	chr11:64667954..64670193-chr11:64843590..64845831,2	K562	blood:
3	chr11:64779777..64783339-chr11:64843637..64848045,5	K562	blood:
4	chr11:64544278..64546281-chr11:64845334..64847627,2	MCF-7	breast:
5	chr11:64807338..64809955-chr11:64842641..64845959,3	K562	blood:
6	chr11:64844843..64847340-chr11:64878794..64881424,3	MCF-7	breast:
7	chr11:64784027..64784556-chr11:64845297..64846240,2	MCF-7	breast:
8	chr11:64794454..64796654-chr11:64844978..64846579,2	MCF-7	breast:
9	chr11:64648332..64650222-chr11:64845042..64847763,3	MCF-7	breast:
10	chr11:64781025..64781584-chr11:64845425..64846204,2	MCF-7	breast:
11	chr11:64780038..64784183-chr11:64845056..64847666,6	K562	blood:
12	chr11:64793258..64795332-chr11:64844721..64846690,2	K562	blood:
13	chr11:64780674..64781293-chr11:64845300..64846312,4	K562	blood:
14	chr11:64780323..64782642-chr11:64844245..64845963,2	MCF-7	breast:
15	chr11:64780696..64782064-chr11:64845315..64846684,8	MCF-7	breast:
16	chr11:64844285..64846947-chr11:64888337..64891082,3	K562	blood:
17	chr11:64783090..64786003-chr11:64844320..64846596,3	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000168061	Chromatin interaction
ENSG00000273003	Chromatin interaction
ENSG00000213465	Chromatin interaction
ENSG00000168066	Chromatin interaction
ENSG00000149792	Chromatin interaction
ENSG00000230835	Chromatin interaction
ENSG00000270775	Chromatin interaction
ENSG00000149806	Chromatin interaction
ENSG00000110025	Chromatin interaction
ENSG00000149809	Chromatin interaction
ENSG00000254501	Chromatin interaction

Extended variants
information (count: 34 )
Associated
traits (count: 6 )

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

rs_ID	r²[population]
rs11227118	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11227120	1.00[CHB][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs11231929	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]
rs1196048	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2282498	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2458298	0.81[CEU][hapmap]
rs2507814	0.83[JPT][hapmap]
rs36057475	0.99[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];0.92[ASN][1000 genomes]
rs3825073	0.86[CHB][hapmap]
rs3862374	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]
rs475089	0.91[EUR][1000 genomes]
rs477539	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]
rs484182	0.96[CEU][hapmap];0.94[CHB][hapmap];1.00[JPT][hapmap]
rs486984	0.82[JPT][hapmap]
rs496427	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs498636	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs502333	0.84[JPT][hapmap]
rs532373	0.96[CEU][hapmap];0.81[ASN][1000 genomes]
rs534236	0.88[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.91[GIH][hapmap];1.00[JPT][hapmap];0.84[TSI][hapmap];0.81[ASN][1000 genomes]
rs548150	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs559644	0.81[ASN][1000 genomes]
rs564966	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs566908	0.87[ASW][hapmap]
rs653111	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];0.92[TSI][hapmap];0.80[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6591869	0.96[CEU][hapmap];0.94[CHB][hapmap];0.90[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[TSI][hapmap];0.81[ASN][1000 genomes]
rs7943007	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs947799	0.92[CEU][hapmap];0.82[CHB][hapmap];0.98[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.90[TSI][hapmap];0.91[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs9971546	1.00[CHB][hapmap];0.89[CHD][hapmap];1.00[JPT][hapmap];0.92[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:6)

SNP	Gene	Cis/trans	Tissue	Source
rs489489	RAB1B	cis	parietal	SCAN
rs489489	SNX15	cis	Muscle Skeletal	GTEx
rs489489	SNX15	cis	parietal	SCAN
rs489489	SCGB2A2	cis	cerebellum	SCAN
rs489489	SPDYC	cis	parietal	SCAN
rs489489	RPS6KA4	cis	lymphoblastoid	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr11:64822400-64850800	Weak transcription	Esophagus	oesophagus
2	chr11:64833600-64845600	Weak transcription	Duodenum Mucosa	Duodenum
3	chr11:64834200-64850600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
4	chr11:64834600-64846200	Weak transcription	Placenta Amnion	Placenta Amnion
5	chr11:64834800-64847800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
6	chr11:64837400-64848000	Weak transcription	Primary monocytes fromperipheralblood	blood
7	chr11:64837600-64845600	Weak transcription	Fetal Intestine Large	intestine
8	chr11:64837800-64846800	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
9	chr11:64837800-64850800	Weak transcription	Pancreas	Pancrea
10	chr11:64839800-64847800	Weak transcription	HSMM	muscle
11	chr11:64840200-64845600	Weak transcription	Primary B cells from peripheral blood	blood
12	chr11:64840200-64850800	Weak transcription	Spleen	Spleen
13	chr11:64841400-64846600	Weak transcription	Fetal Brain Female	brain
14	chr11:64841400-64848400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr11:64841600-64846000	Weak transcription	Muscle Satellite Cultured Cells	--
16	chr11:64842200-64847800	Weak transcription	HUVEC	blood vessel
17	chr11:64842800-64845600	Weak transcription	NH-A	brain
18	chr11:64842800-64846200	Weak transcription	Placenta	Placenta
19	chr11:64842800-64850200	Weak transcription	Fetal Lung	lung
20	chr11:64843000-64849800	Strong transcription	H1 Cell Line	embryonic stem cell
21	chr11:64843000-64849800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
22	chr11:64843000-64849800	Strong transcription	Thymus	Thymus
23	chr11:64843000-64850000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr11:64843000-64850200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
25	chr11:64843000-64850200	Strong transcription	HUES6 Cell Line	embryonic stem cell
26	chr11:64843200-64845600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
27	chr11:64843200-64846000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
28	chr11:64843200-64846000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
29	chr11:64843200-64847200	Strong transcription	Primary neutrophils fromperipheralblood	blood
30	chr11:64843200-64848000	Strong transcription	NHEK	skin
31	chr11:64843200-64849200	Strong transcription	Fetal Muscle Leg	muscle
32	chr11:64843200-64849400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr11:64843200-64849600	Strong transcription	Fetal Stomach	stomach
34	chr11:64843200-64849800	Strong transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr11:64843200-64849800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
36	chr11:64843200-64850200	Strong transcription	HUES64 Cell Line	embryonic stem cell
37	chr11:64843400-64845600	Strong transcription	Fetal Thymus	thymus
38	chr11:64843400-64845800	Weak transcription	NHDF-Ad	bronchial
39	chr11:64843400-64849800	Strong transcription	H9 Cell Line	embryonic stem cell
40	chr11:64843400-64849800	Strong transcription	Fetal Muscle Trunk	muscle
41	chr11:64843400-64850000	Strong transcription	HUES48 Cell Line	embryonic stem cell
42	chr11:64843400-64850200	Strong transcription	iPS-20b Cell Line	embryonic stem cell
43	chr11:64843600-64845600	Strong transcription	Fetal Intestine Small	intestine
44	chr11:64843600-64850600	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
45	chr11:64843800-64845800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
46	chr11:64843800-64846000	Strong transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr11:64844000-64848600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
48	chr11:64844000-64849200	Strong transcription	NHLF	lung
49	chr11:64844000-64849600	Strong transcription	Cortex derived primary cultured neurospheres	brain
50	chr11:64844000-64850200	Strong transcription	iPS-18 Cell Line	embryonic stem cell

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