Variant report

Variant	rs11068156
Chromosome Location	chr12:117146646-117146647
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:117145528..117148245-chr12:117152693..117154607,2	K562	blood:
2	chr12:117145990..117148550-chr12:117156531..117158222,2	K562	blood:
3	chr12:117140715..117144764-chr12:117146137..117149297,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000111412	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:11)

rs_ID	r²[population]
rs10507273	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11068157	0.81[ASW][hapmap];0.89[CEU][hapmap];0.87[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];0.90[JPT][hapmap];0.93[LWK][hapmap];0.92[MEX][hapmap];0.95[MKK][hapmap];0.88[TSI][hapmap];0.91[YRI][hapmap];0.92[AFR][1000 genomes];0.90[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068158	0.94[CEU][hapmap];0.87[CHB][hapmap];0.90[JPT][hapmap];0.86[YRI][hapmap];0.90[AFR][1000 genomes];0.88[AMR][1000 genomes];0.93[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11068160	0.84[AFR][1000 genomes];0.85[EUR][1000 genomes]
rs11068161	0.82[EUR][1000 genomes]
rs12367425	0.82[JPT][hapmap]
rs12819414	0.82[CEU][hapmap];0.81[CHB][hapmap];0.90[JPT][hapmap];0.88[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs2101869	0.81[CHB][hapmap];0.97[CHD][hapmap];0.85[GIH][hapmap];0.90[JPT][hapmap];0.80[ASN][1000 genomes]
rs4767439	0.94[CEU][hapmap];0.91[TSI][hapmap];0.82[YRI][hapmap];0.84[EUR][1000 genomes]
rs4767440	0.94[CEU][hapmap];0.89[GIH][hapmap];0.91[TSI][hapmap];0.84[EUR][1000 genomes]
rs756120	0.84[EUR][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	nsv832523	chr12:117090343-117273810	Strong transcription Flanking Active TSS Weak transcription Enhancers Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	19 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs11068156	RNFT2	cis	parietal	SCAN
rs11068156	PHF10	trans	cerebellum	SCAN
rs11068156	MED13L	cis	parietal	SCAN

Chromatin state (count:104 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:117132200-117147000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:117132400-117147000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
3	chr12:117135600-117147000	Weak transcription	Gastric	stomach
4	chr12:117141400-117147200	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr12:117141600-117150000	Weak transcription	H9 Cell Line	embryonic stem cell
6	chr12:117143200-117147000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr12:117144800-117148800	Enhancers	Fetal Thymus	thymus
8	chr12:117144800-117149000	Enhancers	Thymus	Thymus
9	chr12:117145400-117147000	Enhancers	Primary B cells from cord blood	blood
10	chr12:117145400-117147000	Enhancers	Primary B cells from peripheral blood	blood
11	chr12:117145600-117146800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
12	chr12:117145600-117147400	Enhancers	Right Ventricle	heart
13	chr12:117146000-117147000	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr12:117146200-117146800	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
15	chr12:117146200-117147200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
16	chr12:117146200-117147400	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
17	chr12:117146200-117149000	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
18	chr12:117146200-117152000	Weak transcription	Spleen	Spleen
19	chr12:117146400-117146800	Bivalent Enhancer	ES-I3 Cell Line	embryonic stem cell
20	chr12:117146400-117146800	Bivalent Enhancer	IMR90 fetal lung fibroblasts Cell Line	lung
21	chr12:117146400-117146800	Enhancers	Primary hematopoietic stem cells	blood
22	chr12:117146400-117146800	Enhancers	Primary T helper naive cells from peripheral blood	blood
23	chr12:117146400-117146800	Enhancers	Primary T helper cells PMA-I stimulated	--
24	chr12:117146400-117146800	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
25	chr12:117146400-117146800	Enhancers	Rectal Smooth Muscle	rectum
26	chr12:117146400-117146800	Enhancers	Skeletal Muscle Female	skeletal muscle
27	chr12:117146400-117147000	Enhancers	Primary hematopoietic stem cells short term culture	blood
28	chr12:117146400-117147000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
29	chr12:117146400-117147000	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
30	chr12:117146400-117147000	Enhancers	GM12878-XiMat	blood
31	chr12:117146400-117147200	Enhancers	Primary T helper cells fromperipheralblood	blood
32	chr12:117146400-117147200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr12:117146400-117147200	Bivalent Enhancer	Fetal Heart	heart
34	chr12:117146400-117147200	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
35	chr12:117146400-117147400	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:117146400-117147400	Enhancers	Breast Myoepithelial Primary Cells	Breast
37	chr12:117146400-117147400	Flanking Active TSS	Brain Inferior Temporal Lobe	brain
38	chr12:117146400-117147400	Flanking Active TSS	Brain Substantia Nigra	brain
39	chr12:117146400-117147400	Enhancers	Lung	lung
40	chr12:117146400-117147400	Bivalent Enhancer	NH-A	brain
41	chr12:117146400-117147600	Flanking Active TSS	Brain Cingulate Gyrus	brain
42	chr12:117146400-117147600	Flanking Active TSS	Brain Hippocampus Middle	brain
43	chr12:117146400-117147600	Enhancers	HSMMtube	muscle
44	chr12:117146400-117147800	Flanking Active TSS	Brain Anterior Caudate	brain
45	chr12:117146400-117147800	Bivalent Enhancer	Fetal Muscle Leg	muscle
46	chr12:117146400-117148000	Flanking Active TSS	Brain Germinal Matrix	brain
47	chr12:117146400-117148600	Flanking Active TSS	Fetal Brain Female	brain
48	chr12:117146400-117149000	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
49	chr12:117146600-117146800	Bivalent Enhancer	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
50	chr12:117146600-117146800	Flanking Bivalent TSS/Enh	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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