Variant report

Variant	rs11169154
Chromosome Location	chr12:50171926-50171927
allele	G/T
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	chr12:50170142..50172988-chr12:50230634..50232481,2	MCF-7	breast:
2	chr12:50170539..50173499-chr12:50194309..50196084,2	MCF-7	breast:
3	chr12:50171566..50172481-chr12:50232494..50233075,6	MCF-7	breast:
4	chr12:50031633..50033303-chr12:50170292..50172237,2	MCF-7	breast:
5	chr12:50170723..50173215-chr12:50235786..50237664,2	MCF-7	breast:
6	chr12:50038102..50038980-chr12:50171749..50172585,3	K562	blood:
7	chr12:50170376..50172143-chr12:50258394..50260601,2	K562	blood:
8	chr12:50170135..50173080-chr12:50221067..50223815,3	K562	blood:
9	chr12:50167519..50174148-chr12:50230304..50237815,12	MCF-7	breast:
10	chr12:50170747..50172720-chr12:50179303..50181263,2	K562	blood:
11	chr12:50134836..50135546-chr12:50171623..50172147,2	MCF-7	breast:
12	chr12:50134293..50136830-chr12:50171612..50173479,2	K562	blood:
13	chr12:50170407..50172226-chr12:50230381..50232987,2	K562	blood:
14	chr12:50171688..50172586-chr12:50232580..50233542,2	K562	blood:
15	chr12:50038093..50038993-chr12:50171692..50172608,3	MCF-7	breast:
16	chr12:50171445..50173628-chr12:50220779..50222982,3	MCF-7	breast:
17	chr12:49995716..49998713-chr12:50171804..50173313,2	MCF-7	breast:

No data

Variant related genes	Relation type
ENSG00000161791	Chromatin interaction
ENSG00000167566	Chromatin interaction
ENSG00000186666	Chromatin interaction
ENSG00000258057	Chromatin interaction
ENSG00000139644	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 0)

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

rs_ID	r²[population]
rs11169150	0.81[AMR][1000 genomes]
rs11169153	0.98[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169155	0.87[AMR][1000 genomes]
rs11169156	0.86[AMR][1000 genomes]
rs11169160	1.00[CEU][hapmap];0.87[CHB][hapmap];0.92[MEX][hapmap];0.92[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs11169172	1.00[CEU][hapmap];0.82[AMR][1000 genomes]
rs1470907	0.94[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs1470908	0.84[AMR][1000 genomes]
rs3741554	1.00[CEU][hapmap];0.82[CHB][hapmap];0.85[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs3741555	1.00[CEU][hapmap];0.83[CHB][hapmap];0.82[GIH][hapmap];0.92[MEX][hapmap];0.85[TSI][hapmap];0.86[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs3813526	1.00[CEU][hapmap];0.82[GIH][hapmap];0.87[MEX][hapmap];0.84[MKK][hapmap];0.85[TSI][hapmap];0.85[YRI][hapmap];0.92[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4898531	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes]
rs4898533	1.00[CEU][hapmap];0.84[AMR][1000 genomes]
rs59429669	0.82[AMR][1000 genomes]
rs7134749	1.00[CEU][hapmap];0.82[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs897059	1.00[CEU][hapmap];0.92[MEX][hapmap];0.89[AMR][1000 genomes];0.87[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:2 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1045327	chr12:49975040-50551375	Strong transcription Weak transcription Enhancers Genic enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases
2	nsv541490	chr12:49975040-50551375	Weak transcription Transcr. at gene 5' and 3' Enhancers Genic enhancers Active TSS Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	170 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50158800-50181600	Weak transcription	Brain Hippocampus Middle	brain
2	chr12:50159200-50172200	Weak transcription	Skeletal Muscle Female	skeletal muscle
3	chr12:50159200-50177600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
4	chr12:50159400-50178600	Weak transcription	Right Ventricle	heart
5	chr12:50159800-50172000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
6	chr12:50160000-50172000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr12:50160600-50183400	Weak transcription	Primary T cells from cord blood	blood
8	chr12:50169600-50172200	Enhancers	Fetal Thymus	thymus
9	chr12:50169800-50172000	Weak transcription	Pancreas	Pancrea
10	chr12:50170000-50172000	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
11	chr12:50170000-50172200	Enhancers	GM12878-XiMat	blood
12	chr12:50170000-50172400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr12:50170000-50184800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr12:50170200-50172000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr12:50170200-50172000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr12:50170200-50172200	Enhancers	Primary neutrophils fromperipheralblood	blood
17	chr12:50170200-50172400	Enhancers	NHEK	skin
18	chr12:50170200-50184400	Weak transcription	Brain Cingulate Gyrus	brain
19	chr12:50170600-50172000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr12:50170600-50172000	Enhancers	HMEC	breast
21	chr12:50170600-50172000	Weak transcription	NH-A	brain
22	chr12:50170600-50172200	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
23	chr12:50170800-50176600	Weak transcription	Fetal Muscle Leg	muscle
24	chr12:50170800-50191200	Weak transcription	Brain Substantia Nigra	brain
25	chr12:50171000-50172000	Weak transcription	Primary monocytes fromperipheralblood	blood
26	chr12:50171400-50172200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
27	chr12:50171400-50172400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
28	chr12:50171400-50172400	Enhancers	HepG2	liver
29	chr12:50171600-50172000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
30	chr12:50171600-50172000	Active TSS	Foreskin Fibroblast Primary Cells skin02	Skin
31	chr12:50171600-50172200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr12:50171600-50172400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
33	chr12:50171600-50172400	Enhancers	Primary T helper naive cells from peripheral blood	blood
34	chr12:50171600-50172400	Enhancers	Primary T helper cells PMA-I stimulated	--
35	chr12:50171600-50172400	Enhancers	Primary T helper cells fromperipheralblood	blood
36	chr12:50171600-50172400	Enhancers	Esophagus	oesophagus
37	chr12:50171600-50172400	Enhancers	K562	blood
38	chr12:50171600-50172800	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
39	chr12:50171800-50172000	Enhancers	ES-WA7 Cell Line	embryonic stem cell
40	chr12:50171800-50172000	Enhancers	Primary B cells from cord blood	blood
41	chr12:50171800-50172000	Enhancers	Primary B cells from peripheral blood	blood
42	chr12:50171800-50172000	Enhancers	Brain Anterior Caudate	brain
43	chr12:50171800-50172000	Enhancers	Stomach Mucosa	stomach
44	chr12:50171800-50172000	Flanking Active TSS	Hela-S3	cervix
45	chr12:50171800-50172200	Enhancers	ES-I3 Cell Line	embryonic stem cell
46	chr12:50171800-50172200	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:50171800-50172200	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
48	chr12:50171800-50172200	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
49	chr12:50171800-50172200	Enhancers	Primary T killer memory cells from peripheral blood	blood
50	chr12:50171800-50172200	Bivalent Enhancer	Rectal Mucosa Donor 31	rectum

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