Variant report

Variant	rs11169490
Chromosome Location	chr12:50939276-50939277
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:50938363..50942077-chr12:50942741..50946423,3	MCF-7	breast:
2	chr12:50938291..50940532-chr12:50951166..50953064,2	MCF-7	breast:
3	chr12:50937236..50940218-chr12:50942824..50944458,2	K562	blood:

Extended variants
information (count: 56 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:55)

rs_ID	r²[population]
rs10747583	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10783375	0.94[ASN][1000 genomes]
rs10876045	0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876055	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876059	0.91[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs10876066	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10876069	0.82[AFR][1000 genomes];0.84[AMR][1000 genomes];0.83[ASN][1000 genomes]
rs10876074	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs11169453	0.93[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169470	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11169484	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs11169486	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169492	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169506	0.86[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs11169523	0.89[AMR][1000 genomes]
rs11169524	0.90[AMR][1000 genomes]
rs12307178	0.88[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12372538	0.87[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12425362	0.87[AFR][1000 genomes];0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs12427378	0.90[AMR][1000 genomes]
rs12582683	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.93[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12814717	0.90[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12818741	0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs12825915	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs1316442	0.85[AMR][1000 genomes]
rs1316607	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs13378012	0.86[AMR][1000 genomes]
rs1967576	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs2090852	0.90[AMR][1000 genomes]
rs2139930	0.90[AMR][1000 genomes]
rs2243571	0.81[ASN][1000 genomes]
rs2280503	0.83[AMR][1000 genomes]
rs34553264	0.90[AMR][1000 genomes]
rs34682944	0.84[AMR][1000 genomes];0.83[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs3742062	0.86[AMR][1000 genomes]
rs3935138	0.97[ASN][1000 genomes]
rs3935870	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4617661	0.95[ASN][1000 genomes]
rs4768847	0.94[ASN][1000 genomes]
rs61699126	0.90[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61926278	0.85[AMR][1000 genomes]
rs6580756	0.94[ASN][1000 genomes]
rs67092086	0.98[ASN][1000 genomes]
rs7133160	0.88[AMR][1000 genomes]
rs7133687	0.94[AMR][1000 genomes];0.91[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7137845	0.88[AMR][1000 genomes]
rs7298661	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs7298665	0.88[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs7302435	0.88[AMR][1000 genomes]
rs7305375	0.84[ASN][1000 genomes]
rs7316864	0.97[ASN][1000 genomes]
rs7397999	0.97[ASN][1000 genomes]
rs7487429	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs7965652	0.88[AMR][1000 genomes]
rs9788075	0.88[AMR][1000 genomes];0.85[EUR][1000 genomes];0.85[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv1820967	chr12:50856613-51002088	Flanking Active TSS Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	7 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs11169490	ATF1	cis	Artery Tibial	GTEx
rs11169490	CERS5	cis	Nerve Tibial	GTEx
rs11169490	ATF1	cis	Adipose Subcutaneous	GTEx
rs11169490	ATF1	cis	Esophagus Muscularis	GTEx
rs11169490	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50911600-50939800	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
2	chr12:50920200-50939600	Weak transcription	Fetal Heart	heart
3	chr12:50920800-50939400	Weak transcription	Fetal Brain Female	brain
4	chr12:50920800-50939800	Weak transcription	Fetal Brain Male	brain
5	chr12:50920800-50962400	Weak transcription	Stomach Smooth Muscle	stomach
6	chr12:50921000-50939400	Weak transcription	Fetal Muscle Trunk	muscle
7	chr12:50921000-50940200	Weak transcription	Rectal Smooth Muscle	rectum
8	chr12:50921200-50939800	Weak transcription	Brain Germinal Matrix	brain
9	chr12:50923400-50939800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
10	chr12:50923600-50939600	Weak transcription	Skeletal Muscle Female	skeletal muscle
11	chr12:50927200-50957600	Weak transcription	Fetal Lung	lung
12	chr12:50927400-50939600	Weak transcription	Thymus	Thymus
13	chr12:50927400-50939800	Weak transcription	Colon Smooth Muscle	Colon
14	chr12:50927400-50944400	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
15	chr12:50927400-50948800	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
16	chr12:50927400-50951000	Weak transcription	Dnd41	blood
17	chr12:50927400-50961800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
18	chr12:50927600-50941600	Weak transcription	Pancreas	Pancrea
19	chr12:50927600-50950000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
20	chr12:50927600-50957200	Weak transcription	Spleen	Spleen
21	chr12:50927800-50947600	Weak transcription	Fetal Thymus	thymus
22	chr12:50927800-50961800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr12:50929000-50939600	Weak transcription	Ovary	ovary
24	chr12:50929200-50939600	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
25	chr12:50929200-50943800	Weak transcription	Placenta	Placenta
26	chr12:50930600-50948600	Weak transcription	Left Ventricle	heart
27	chr12:50931600-50939600	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr12:50932000-50945200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
29	chr12:50932000-50957800	Weak transcription	Duodenum Smooth Muscle	Duodenum
30	chr12:50932000-50958000	Weak transcription	Adipose Nuclei	Adipose
31	chr12:50932200-50939400	Weak transcription	Osteobl	bone
32	chr12:50932200-50939800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
33	chr12:50932200-50948400	Weak transcription	Primary T cells from cord blood	blood
34	chr12:50932200-50948600	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
35	chr12:50932200-50961800	Weak transcription	Right Ventricle	heart
36	chr12:50932400-50939800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr12:50932400-50941600	Weak transcription	Colonic Mucosa	Colon
38	chr12:50932400-50944400	Weak transcription	Primary hematopoietic stem cells short term culture	blood
39	chr12:50932400-50949000	Weak transcription	Primary hematopoietic stem cells	blood
40	chr12:50932800-50939800	Weak transcription	Brain Anterior Caudate	brain
41	chr12:50932800-50947600	Weak transcription	Primary B cells from peripheral blood	blood
42	chr12:50932800-50948200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
43	chr12:50933000-50939400	Weak transcription	Primary monocytes fromperipheralblood	blood
44	chr12:50933000-50952400	Weak transcription	Primary B cells from cord blood	blood
45	chr12:50933400-50939600	Weak transcription	H1 Cell Line	embryonic stem cell
46	chr12:50933800-50939800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
47	chr12:50933800-50940200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
48	chr12:50935400-50939800	Weak transcription	Primary T helper naive cells from peripheral blood	blood
49	chr12:50935800-50944600	Weak transcription	Esophagus	oesophagus
50	chr12:50935800-50948400	Weak transcription	Primary T cells fromperipheralblood	blood

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