Variant report

Variant	rs11169315
Chromosome Location	chr12:50595263-50595264
allele	A/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	TCF12	chr12:50594148-50595289	SK-N-SH	brain:	n/a	n/a
2	GATA3	chr12:50594142-50595352	SK-N-SH	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr12:50594550..50596135-chr12:50613800..50616360,2	K562	blood:
2	chr12:50477720..50479464-chr12:50594213..50596665,2	MCF-7	breast:
3	chr12:50593299..50595374-chr12:50677220..50679734,2	K562	blood:

Variant related genes	Relation type
LIMA1	TF binding region
ENSG00000066117	Chromatin interaction
ENSG00000050405	Chromatin interaction
ENSG00000203433	Chromatin interaction

Extended variants
information (count: 125 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:122)

rs_ID	r²[population]
rs10506292	1.00[CEU][hapmap];0.82[ASN][1000 genomes]
rs10783344	1.00[CEU][hapmap];0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs10783349	0.82[EUR][1000 genomes]
rs10876013	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs10876014	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876015	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876016	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876017	1.00[CEU][hapmap];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs10876023	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs10876024	1.00[CEU][hapmap]
rs11169314	0.84[CEU][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11169317	0.98[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11169319	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs11169322	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11169331	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169332	1.00[CEU][hapmap];0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs11169335	1.00[CEU][hapmap];0.81[AFR][1000 genomes];0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs11169339	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11169345	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169347	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169348	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169349	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169350	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169351	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11169357	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169359	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169360	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11169367	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169369	0.84[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169370	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169371	0.81[EUR][1000 genomes]
rs11169373	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169374	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11169375	0.83[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs11169376	0.83[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs11169377	0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11169390	0.80[ASN][1000 genomes]
rs11833608	0.96[CEU][hapmap]
rs11836169	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11838347	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs12299758	0.82[ASN][1000 genomes]
rs12303082	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs12367872	1.00[CEU][hapmap]
rs12422417	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs12424691	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12424713	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12425229	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12425705	1.00[CEU][hapmap];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs12426444	0.81[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs12811291	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12814094	0.80[ASN][1000 genomes]
rs12821454	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs12823506	0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12828340	1.00[CEU][hapmap];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs12832940	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs1362983	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17124562	0.93[AMR][1000 genomes];0.96[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs1972611	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs1984993	0.82[ASN][1000 genomes]
rs2009072	0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2111988	1.00[CEU][hapmap];0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2302900	0.96[CEU][hapmap];0.89[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2358539	1.00[CEU][hapmap];0.92[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28628775	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs34039674	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34614542	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs34825838	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs34849043	0.81[AMR][1000 genomes];0.85[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs34858415	0.81[AMR][1000 genomes];0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35209607	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35535298	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs35768991	0.89[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs35878271	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs35933908	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs3812825	1.00[CEU][hapmap];0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3861100	1.00[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4348979	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs4421818	1.00[CEU][hapmap];0.80[ASN][1000 genomes]
rs4768872	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768949	0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs4768951	0.92[CEU][hapmap]
rs6580730	0.92[AMR][1000 genomes];0.85[ASN][1000 genomes]
rs6580735	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs6580736	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6580737	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs6580738	0.96[CEU][hapmap];0.83[EUR][1000 genomes]
rs6580739	0.84[AMR][1000 genomes];0.84[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs6580740	0.81[EUR][1000 genomes]
rs6580741	0.81[AMR][1000 genomes];0.82[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs67138019	0.86[EUR][1000 genomes]
rs7132551	1.00[CEU][hapmap];0.84[AFR][1000 genomes];0.96[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7134595	1.00[CEU][hapmap]
rs7135777	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7138420	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7138622	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs71465002	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7295847	0.82[ASN][1000 genomes]
rs7296291	1.00[CEU][hapmap];0.82[ASN][1000 genomes]
rs7302363	0.80[ASN][1000 genomes]
rs7304445	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7305995	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7308095	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7308885	0.96[AMR][1000 genomes];0.96[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7310541	0.84[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7311378	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7311491	0.81[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7311973	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7312252	1.00[CEU][hapmap];0.82[ASN][1000 genomes]
rs7314465	0.90[AFR][1000 genomes];1.00[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7315690	0.96[CEU][hapmap];0.81[EUR][1000 genomes]
rs7315871	0.80[EUR][1000 genomes]
rs7315955	0.83[AMR][1000 genomes];0.82[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7485486	0.81[EUR][1000 genomes]
rs7486747	1.00[CEU][hapmap];0.89[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7488682	0.84[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7953953	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7956468	0.85[AMR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7974648	0.81[AMR][1000 genomes];0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7979830	1.00[CEU][hapmap];0.90[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7980911	0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9705460	0.84[AMR][1000 genomes];0.88[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9739363	0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:3 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	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
2	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
3	nsv899075	chr12:50594947-50835060	Flanking Active TSS Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs11169315	CERS5	cis	Nerve Tibial	GTEx
rs11169315	DIP2B	cis	multi-tissue	Pritchard
rs11169315	KIAA1463	cis	multi-tissue	Pritchard
rs11169315	DIP2B	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:122 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:50562200-50597000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
2	chr12:50564400-50600800	Weak transcription	Primary monocytes fromperipheralblood	blood
3	chr12:50570000-50601400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:50571800-50595800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
5	chr12:50571800-50597000	Weak transcription	Thymus	Thymus
6	chr12:50571800-50597600	Weak transcription	Monocytes-CD14+_RO01746	blood
7	chr12:50571800-50614200	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr12:50572200-50614000	Weak transcription	Right Ventricle	heart
9	chr12:50579600-50598000	Weak transcription	Brain Cingulate Gyrus	brain
10	chr12:50580400-50595800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
11	chr12:50581800-50601000	Weak transcription	Brain Substantia Nigra	brain
12	chr12:50582000-50596000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr12:50582400-50596200	Weak transcription	Brain Inferior Temporal Lobe	brain
14	chr12:50582400-50598200	Weak transcription	Brain Hippocampus Middle	brain
15	chr12:50582400-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
16	chr12:50582600-50597000	Weak transcription	Fetal Brain Female	brain
17	chr12:50582600-50598000	Weak transcription	Psoas Muscle	Psoas
18	chr12:50582600-50598200	Weak transcription	Pancreas	Pancrea
19	chr12:50582800-50614000	Weak transcription	Brain Angular Gyrus	brain
20	chr12:50582800-50614200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
21	chr12:50583000-50614400	Weak transcription	Brain Anterior Caudate	brain
22	chr12:50583400-50598200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
23	chr12:50583400-50600800	Strong transcription	Adipose Nuclei	Adipose
24	chr12:50584600-50595400	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:50584600-50595800	Strong transcription	HUES48 Cell Line	embryonic stem cell
26	chr12:50584600-50596400	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
27	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
28	chr12:50585200-50604000	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
29	chr12:50586000-50599600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
30	chr12:50586800-50595800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
31	chr12:50586800-50596000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
32	chr12:50587000-50597600	Weak transcription	Skeletal Muscle Female	skeletal muscle
33	chr12:50587800-50599800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
34	chr12:50588000-50599800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
35	chr12:50588400-50599600	Strong transcription	Primary T helper cells fromperipheralblood	blood
36	chr12:50588400-50600200	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
37	chr12:50588400-50600600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr12:50588400-50600600	Strong transcription	Primary T cells fromperipheralblood	blood
39	chr12:50589000-50595800	Strong transcription	HUES64 Cell Line	embryonic stem cell
40	chr12:50589400-50599800	Strong transcription	Primary T helper cells PMA-I stimulated	--
41	chr12:50589400-50599800	Strong transcription	GM12878-XiMat	blood
42	chr12:50589400-50600800	Strong transcription	Cortex derived primary cultured neurospheres	brain
43	chr12:50589600-50598400	Genic enhancers	Osteobl	bone
44	chr12:50590600-50600000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
45	chr12:50590600-50600200	Strong transcription	Fetal Thymus	thymus
46	chr12:50590800-50599800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
47	chr12:50590800-50600000	Weak transcription	Pancreatic Islets	Pancreatic Islet
48	chr12:50591000-50598000	Weak transcription	Brain Germinal Matrix	brain
49	chr12:50591000-50600200	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
50	chr12:50591000-50603000	Strong transcription	Fetal Muscle Trunk	muscle

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