Variant report

Variant	rs11169278
Chromosome Location	chr12:50525787-50525788
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50525700..50528015-chr12:50536583..50539181,2	MCF-7	breast:
2	chr12:50524715..50526452-chr12:50529761..50531846,2	K562	blood:
3	chr12:50515617..50517126-chr12:50524632..50526499,2	K562	blood:
4	chr12:50525406..50528688-chr12:50558864..50561981,4	MCF-7	breast:

Variant related genes	Relation type
ENSG00000139624	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

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

rs_ID	r²[population]
rs10735824	0.85[AMR][1000 genomes];0.88[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs10783338	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs10876000	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169281	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169282	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12369049	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12369104	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12819883	0.88[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1554844	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1554845	1.00[AFR][1000 genomes];0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17124432	0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2204683	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs34167640	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs3741562	0.87[AFR][1000 genomes];0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59262224	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs6580728	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs66782120	0.85[ASN][1000 genomes]
rs7135322	0.81[AFR][1000 genomes];0.95[AMR][1000 genomes];0.93[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7138945	0.85[AMR][1000 genomes];0.94[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7294618	0.93[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307230	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7307469	0.95[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7308474	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7398567	0.87[AMR][1000 genomes];0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7961065	0.91[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7961112	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7964698	0.86[EUR][1000 genomes]
rs7967979	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7968119	0.82[AFR][1000 genomes];0.85[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7972465	0.87[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs7978904	0.83[AMR][1000 genomes];0.83[EUR][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	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
3	nsv530671	chr12:50233858-50708991	Flanking Active TSS Active TSS Enhancers Weak transcription Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	117 gene(s)	inside rSNPs	diseases
4	esv3392138	chr12:50394642-50645326	Flanking Bivalent TSS/Enh Active TSS Flanking Active TSS Enhancers Weak transcription Strong transcription Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	66 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11169278	CERS5	cis	Muscle Skeletal	GTEx
rs11169278	CERS5	cis	Nerve Tibial	GTEx
rs11169278	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50507000-50537400	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:50507000-50539600	Weak transcription	Stomach Mucosa	stomach
3	chr12:50507200-50532000	Weak transcription	Pancreatic Islets	Pancreatic Islet
4	chr12:50510800-50528400	Strong transcription	Liver	Liver
5	chr12:50511200-50538200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
6	chr12:50511400-50538600	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
7	chr12:50512600-50529200	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr12:50512600-50538200	Strong transcription	Primary B cells from cord blood	blood
9	chr12:50516000-50532400	Strong transcription	Duodenum Mucosa	Duodenum
10	chr12:50516600-50536200	Strong transcription	Fetal Intestine Large	intestine
11	chr12:50517600-50548000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
12	chr12:50518000-50532400	Strong transcription	HSMM	muscle
13	chr12:50519200-50538200	Strong transcription	Fetal Muscle Leg	muscle
14	chr12:50519400-50538400	Strong transcription	Primary T helper cells fromperipheralblood	blood
15	chr12:50519600-50532600	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
16	chr12:50519600-50537800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
17	chr12:50519600-50538200	Strong transcription	Fetal Muscle Trunk	muscle
18	chr12:50520200-50529400	Strong transcription	Fetal Intestine Small	intestine
19	chr12:50520200-50537800	Strong transcription	Primary T cells from cord blood	blood
20	chr12:50520200-50539000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
21	chr12:50520400-50526400	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
22	chr12:50520400-50528400	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
23	chr12:50520400-50529800	Strong transcription	Lung	lung
24	chr12:50520400-50530600	Strong transcription	Fetal Stomach	stomach
25	chr12:50520400-50538000	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
26	chr12:50520600-50525800	Strong transcription	Brain Cingulate Gyrus	brain
27	chr12:50520600-50525800	Strong transcription	Colonic Mucosa	Colon
28	chr12:50520600-50525800	Strong transcription	HMEC	breast
29	chr12:50520600-50526400	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr12:50520600-50526600	Strong transcription	Primary T helper cells PMA-I stimulated	--
31	chr12:50520600-50526600	Strong transcription	Osteobl	bone
32	chr12:50520600-50528400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
33	chr12:50520600-50528400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr12:50520600-50528800	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr12:50520600-50533800	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
36	chr12:50520600-50537400	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr12:50520600-50537800	Strong transcription	HUES6 Cell Line	embryonic stem cell
38	chr12:50520600-50537800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
39	chr12:50520600-50538000	Strong transcription	Primary neutrophils fromperipheralblood	blood
40	chr12:50520600-50538200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
41	chr12:50520600-50538200	Strong transcription	Fetal Thymus	thymus
42	chr12:50520600-50538400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr12:50520600-50538600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
44	chr12:50520600-50538600	Strong transcription	Cortex derived primary cultured neurospheres	brain
45	chr12:50520800-50525800	Strong transcription	NHLF	lung
46	chr12:50520800-50527200	Strong transcription	GM12878-XiMat	blood
47	chr12:50520800-50528600	Strong transcription	Rectal Smooth Muscle	rectum
48	chr12:50520800-50529200	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr12:50520800-50532400	Strong transcription	Sigmoid Colon	Sigmoid Colon
50	chr12:50520800-50532800	Strong transcription	Dnd41	blood

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