Variant report

Variant	rs2299927
Chromosome Location	chr14:78066661-78066662
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr14:78063987..78068208-chr14:78069326..78072935,4	MCF-7	breast:
2	chr14:78065290..78070188-chr14:78072894..78075904,4	K562	blood:
3	chr14:78064657..78067063-chr14:78079647..78083000,3	MCF-7	breast:
4	chr14:78063505..78065787-chr14:78066559..78069226,2	K562	blood:
5	chr14:78057510..78059603-chr14:78066224..78069062,2	MCF-7	breast:
6	chr14:78064498..78067393-chr14:78068632..78070407,3	K562	blood:
7	chr14:78065290..78068119-chr14:78072066..78074474,3	K562	blood:

Variant related genes	Relation type
ENSG00000100596	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:33)

rs_ID	r²[population]
rs10129280	0.81[CHB][hapmap]
rs10139059	0.81[CHB][hapmap]
rs10139852	0.87[ASN][1000 genomes]
rs10140195	1.00[CHB][hapmap];0.94[JPT][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs10148189	0.88[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10873309	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs11626349	0.86[CHD][hapmap]
rs12432164	0.93[ASN][1000 genomes]
rs12587835	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs13379058	0.93[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs176897	0.93[ASN][1000 genomes]
rs176898	0.93[ASN][1000 genomes]
rs176901	1.00[CHB][hapmap];1.00[CHD][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs176903	1.00[CHB][hapmap];0.93[JPT][hapmap];0.93[ASN][1000 genomes]
rs176907	0.91[ASN][1000 genomes]
rs1990806	0.90[CEU][hapmap];1.00[CHB][hapmap];0.93[JPT][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2267746	0.81[CHB][hapmap]
rs2267747	0.81[CHB][hapmap]
rs2267748	0.81[CHB][hapmap]
rs2267749	0.81[CHB][hapmap]
rs2267750	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs2299921	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs2299922	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.99[ASN][1000 genomes]
rs2299924	0.81[CHB][hapmap];0.88[CHD][hapmap]
rs2299928	0.81[CHB][hapmap];0.91[CHD][hapmap]
rs2299929	1.00[CEU][hapmap];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28460392	0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28472502	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs58598324	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7144314	0.91[CEU][hapmap];0.84[CHB][hapmap];0.95[CHD][hapmap];0.97[GIH][hapmap];0.82[TSI][hapmap]
rs7157536	0.98[ASN][1000 genomes]
rs7158771	0.99[ASN][1000 genomes]
rs9944097	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.94[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	nsv832835	chr14:77906706-78095207	Weak transcription Enhancers Strong transcription Genic enhancers Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases
2	nsv1053810	chr14:77987871-78148320	Genic enhancers Active TSS Weak transcription Enhancers Strong transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	20 gene(s)	inside rSNPs	diseases
3	nsv1051554	chr14:78004196-78122980	Enhancers Active TSS Weak transcription Genic enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs2299927	POMT2	cis	cerebellum	SCAN

Chromatin state (count:112 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
3	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
4	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
5	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
6	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
7	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
8	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
9	chr14:78056800-78070000	Weak transcription	Gastric	stomach
10	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
11	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
12	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
13	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
14	chr14:78061600-78070000	Weak transcription	Esophagus	oesophagus
15	chr14:78061800-78069800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
16	chr14:78062200-78068200	Weak transcription	H1 Cell Line	embryonic stem cell
17	chr14:78062200-78070200	Weak transcription	Ovary	ovary
18	chr14:78062800-78075000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr14:78063200-78070000	Weak transcription	Brain Germinal Matrix	brain
20	chr14:78063200-78077800	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr14:78063400-78069400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
22	chr14:78063400-78069400	Weak transcription	Primary neutrophils fromperipheralblood	blood
23	chr14:78063400-78069800	Weak transcription	Liver	Liver
24	chr14:78063400-78070000	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
25	chr14:78063400-78070200	Weak transcription	Fetal Muscle Trunk	muscle
26	chr14:78063400-78070200	Weak transcription	Fetal Thymus	thymus
27	chr14:78063400-78081600	Weak transcription	Fetal Stomach	stomach
28	chr14:78063600-78067800	Weak transcription	HUES6 Cell Line	embryonic stem cell
29	chr14:78063600-78067800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
30	chr14:78063600-78069400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr14:78063600-78069600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr14:78063600-78070200	Weak transcription	Stomach Smooth Muscle	stomach
33	chr14:78063800-78066800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
34	chr14:78063800-78067000	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr14:78063800-78069400	Weak transcription	Brain Cingulate Gyrus	brain
36	chr14:78063800-78071800	Weak transcription	Fetal Lung	lung
37	chr14:78063800-78072000	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
38	chr14:78063800-78074000	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
39	chr14:78063800-78074200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
40	chr14:78064200-78066800	Enhancers	Primary T cells fromperipheralblood	blood
41	chr14:78064400-78067000	Enhancers	Primary B cells from peripheral blood	blood
42	chr14:78064400-78067400	Enhancers	A549	lung
43	chr14:78064600-78066800	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
44	chr14:78064600-78067400	Enhancers	Primary T helper cells fromperipheralblood	blood
45	chr14:78064600-78070600	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
46	chr14:78064800-78066800	Enhancers	Sigmoid Colon	Sigmoid Colon
47	chr14:78064800-78067000	Enhancers	Primary T cells from cord blood	blood
48	chr14:78064800-78067000	Enhancers	Stomach Mucosa	stomach
49	chr14:78064800-78067200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
50	chr14:78064800-78067200	Enhancers	Primary T killer memory cells from peripheral blood	blood

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