Variant report

Variant	rs12435993
Chromosome Location	chr14:78063440-78063441
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 22 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs10132804	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs10139421	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10873310	0.81[ASN][1000 genomes]
rs11159282	0.81[ASN][1000 genomes]
rs11159285	0.80[ASN][1000 genomes]
rs12432127	0.80[ASN][1000 genomes]
rs12586560	0.82[CHD][hapmap]
rs12878099	0.89[CEU][hapmap];0.93[CHB][hapmap];0.94[CHD][hapmap];0.95[GIH][hapmap];1.00[JPT][hapmap];0.87[LWK][hapmap];1.00[MEX][hapmap];0.88[MKK][hapmap];1.00[TSI][hapmap];0.99[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs12880698	0.84[ASN][1000 genomes]
rs12881338	0.87[CHB][hapmap];0.88[CHD][hapmap];0.91[JPT][hapmap];0.81[ASN][1000 genomes]
rs12881530	0.85[CHD][hapmap]
rs2267747	0.88[YRI][hapmap]
rs2267748	0.87[YRI][hapmap]
rs4899664	0.81[ASN][1000 genomes]
rs4903619	0.80[ASN][1000 genomes]
rs56812919	0.86[AMR][1000 genomes];0.96[ASN][1000 genomes]
rs7149026	0.80[ASN][1000 genomes]
rs7153483	0.96[ASN][1000 genomes]
rs7155602	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs12435993	FOS	cis	parietal	SCAN
rs12435993	NEK9	cis	parietal	SCAN
rs12435993	COQ6	cis	cerebellum	SCAN

Chromatin state (count:121 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:78013200-78066200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:78021800-78068400	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr14:78021800-78071600	Weak transcription	Colon Smooth Muscle	Colon
4	chr14:78042400-78066600	Weak transcription	Fetal Brain Female	brain
5	chr14:78047400-78070000	Weak transcription	Fetal Brain Male	brain
6	chr14:78048200-78067200	Weak transcription	Hela-S3	cervix
7	chr14:78049400-78066400	Weak transcription	Skeletal Muscle Male	skeletal muscle
8	chr14:78051400-78066200	Weak transcription	Pancreas	Pancrea
9	chr14:78051400-78070200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr14:78051600-78072600	Weak transcription	Psoas Muscle	Psoas
11	chr14:78055000-78081600	Weak transcription	Right Ventricle	heart
12	chr14:78056600-78072800	Weak transcription	Placenta	Placenta
13	chr14:78056800-78070000	Weak transcription	Gastric	stomach
14	chr14:78057000-78064000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
15	chr14:78057000-78065000	Weak transcription	Lung	lung
16	chr14:78057400-78070000	Weak transcription	Spleen	Spleen
17	chr14:78057600-78081400	Weak transcription	Rectal Smooth Muscle	rectum
18	chr14:78057800-78065000	Weak transcription	Small Intestine	intestine
19	chr14:78058000-78063600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
20	chr14:78058800-78063800	Strong transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
21	chr14:78059000-78063800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr14:78059000-78065800	Weak transcription	Colonic Mucosa	Colon
23	chr14:78060200-78066800	Weak transcription	Pancreatic Islets	Pancreatic Islet
24	chr14:78060200-78069400	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
25	chr14:78060400-78065000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
26	chr14:78060400-78065400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
27	chr14:78060600-78063600	Strong transcription	iPS-20b Cell Line	embryonic stem cell
28	chr14:78060600-78065200	Weak transcription	Fetal Kidney	kidney
29	chr14:78060800-78063600	Strong transcription	HUES6 Cell Line	embryonic stem cell
30	chr14:78060800-78063600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
31	chr14:78060800-78064000	Strong transcription	Muscle Satellite Cultured Cells	--
32	chr14:78061000-78063600	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
33	chr14:78061000-78063800	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
34	chr14:78061000-78063800	Strong transcription	HUES48 Cell Line	embryonic stem cell
35	chr14:78061000-78063800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
36	chr14:78061000-78063800	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
37	chr14:78061000-78063800	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
38	chr14:78061000-78063800	Strong transcription	Adipose Nuclei	Adipose
39	chr14:78061000-78063800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr14:78061000-78063800	Strong transcription	Rectal Mucosa Donor 31	rectum
41	chr14:78061000-78064000	Strong transcription	Fetal Intestine Large	intestine
42	chr14:78061000-78064000	Strong transcription	Rectal Mucosa Donor 29	rectum
43	chr14:78061000-78064400	Strong transcription	Fetal Muscle Leg	muscle
44	chr14:78061200-78063600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr14:78061200-78063600	Strong transcription	Stomach Smooth Muscle	stomach
46	chr14:78061200-78063600	Strong transcription	GM12878-XiMat	blood
47	chr14:78061200-78063800	Strong transcription	iPS-18 Cell Line	embryonic stem cell
48	chr14:78061200-78063800	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr14:78061200-78063800	Strong transcription	NH-A	brain
50	chr14:78061200-78063800	Strong transcription	Osteobl	bone

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