Variant report

Variant	rs2936840
Chromosome Location	chr12:118578843-118578844
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr12:118577698..118580180-chr12:118811113..118813216,2	MCF-7	breast:
2	chr12:118574074..118576910-chr12:118577432..118580343,3	K562	blood:

Variant related genes	Relation type
ENSG00000089220	Chromatin interaction

Extended variants
information (count: 18 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:15)

rs_ID	r²[population]
rs1051470	0.81[GIH][hapmap]
rs12423154	1.00[JPT][hapmap];0.88[ASN][1000 genomes]
rs12423959	0.88[ASN][1000 genomes]
rs191626	0.81[GIH][hapmap]
rs2017414	0.82[ASN][1000 genomes]
rs3847652	1.00[CHB][hapmap];0.80[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs56070243	0.83[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs61943518	0.86[ASN][1000 genomes]
rs61943519	0.88[ASN][1000 genomes]
rs61943521	0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73217996	0.82[ASN][1000 genomes]
rs7956285	1.00[CHB][hapmap];0.94[GIH][hapmap];1.00[JPT][hapmap];0.91[MKK][hapmap];0.82[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7961197	0.82[ASN][1000 genomes]
rs7970036	0.81[AFR][1000 genomes];0.82[AMR][1000 genomes];0.80[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs904662	0.85[GIH][hapmap]

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	nsv1053785	chr12:118490955-118874194	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	37 gene(s)	inside rSNPs	diseases
2	nsv1054703	chr12:118575000-118638613	Active TSS Strong transcription Weak transcription Flanking Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Enhancers Bivalent Enhancer 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
3	nsv541611	chr12:118575000-118638613	Weak transcription Strong transcription Active TSS Flanking Active TSS Enhancers Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer 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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs2936840	PEBP1	cis	cerebellum	SCAN
rs2936840	PEBP1	cis	lymphoblastoid	seeQTL

Chromatin state (count:125 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:118575000-118585200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr12:118575200-118579400	Weak transcription	Primary B cells from cord blood	blood
3	chr12:118575200-118585800	Weak transcription	Fetal Heart	heart
4	chr12:118575400-118584800	Strong transcription	NHEK	skin
5	chr12:118575400-118590400	Strong transcription	Fetal Muscle Trunk	muscle
6	chr12:118575400-118590600	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
7	chr12:118575400-118590600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr12:118575400-118591400	Strong transcription	Fetal Stomach	stomach
9	chr12:118575600-118584000	Strong transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:118575600-118584000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr12:118575600-118585600	Strong transcription	H9 Cell Line	embryonic stem cell
12	chr12:118575600-118586800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
13	chr12:118575600-118588200	Strong transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:118575600-118601600	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
15	chr12:118575800-118580000	Strong transcription	HUVEC	blood vessel
16	chr12:118575800-118584000	Strong transcription	iPS DF 6.9 Cell Line	embryonic stem cell
17	chr12:118575800-118584200	Strong transcription	Fetal Brain Female	brain
18	chr12:118575800-118584200	Strong transcription	A549	lung
19	chr12:118575800-118585600	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
20	chr12:118575800-118587800	Strong transcription	HUES64 Cell Line	embryonic stem cell
21	chr12:118575800-118589200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
22	chr12:118575800-118590400	Strong transcription	Lung	lung
23	chr12:118575800-118590600	Strong transcription	Fetal Muscle Leg	muscle
24	chr12:118575800-118590800	Strong transcription	Rectal Mucosa Donor 29	rectum
25	chr12:118576000-118585000	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
26	chr12:118576000-118585400	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
27	chr12:118576000-118585600	Strong transcription	H1 Cell Line	embryonic stem cell
28	chr12:118576000-118585600	Strong transcription	Osteobl	bone
29	chr12:118576000-118586800	Strong transcription	iPS-20b Cell Line	embryonic stem cell
30	chr12:118576000-118587200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
31	chr12:118576000-118591600	Strong transcription	Fetal Intestine Large	intestine
32	chr12:118576000-118591600	Strong transcription	Dnd41	blood
33	chr12:118576000-118601200	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
34	chr12:118576000-118619600	Strong transcription	Primary hematopoietic stem cells short term culture	blood
35	chr12:118576000-118624000	Weak transcription	Stomach Mucosa	stomach
36	chr12:118576200-118585000	Strong transcription	Primary T cells fromperipheralblood	blood
37	chr12:118576200-118586600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
38	chr12:118576200-118587600	Strong transcription	HUES6 Cell Line	embryonic stem cell
39	chr12:118576200-118590400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
40	chr12:118576200-118590600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
41	chr12:118576200-118591000	Strong transcription	Breast Myoepithelial Primary Cells	Breast
42	chr12:118576200-118591400	Strong transcription	Primary T helper cells fromperipheralblood	blood
43	chr12:118576200-118595400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
44	chr12:118576400-118584000	Strong transcription	Primary T cells from cord blood	blood
45	chr12:118576400-118591400	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr12:118576600-118584200	Strong transcription	Colon Smooth Muscle	Colon
47	chr12:118576600-118585200	Strong transcription	Rectal Smooth Muscle	rectum
48	chr12:118576600-118585600	Strong transcription	Duodenum Mucosa	Duodenum
49	chr12:118576600-118587600	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
50	chr12:118576600-118590600	Strong transcription	Adipose Nuclei	Adipose

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