Variant report

Variant	rs12435399
Chromosome Location	chr14:104063912-104063913
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:104056281..104057998-chr14:104062003..104064043,2	K562	blood:

Extended variants
information (count: 61 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:52)

rs_ID	r²[population]
rs10047805	0.80[ASN][1000 genomes]
rs1078756	0.91[AMR][1000 genomes];1.00[ASN][1000 genomes]
rs11160754	0.87[AMR][1000 genomes];0.97[ASN][1000 genomes]
rs11160755	0.81[AMR][1000 genomes]
rs11626589	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs11848721	0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs11850979	0.81[ASN][1000 genomes]
rs12431809	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12433529	0.81[AMR][1000 genomes]
rs12434218	0.82[AMR][1000 genomes];0.81[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12879004	0.85[EUR][1000 genomes]
rs12897511	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28798508	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs28823639	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs2896488	0.86[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2896489	0.82[ASN][1000 genomes]
rs34258128	0.82[EUR][1000 genomes]
rs34259310	0.80[EUR][1000 genomes]
rs35686878	0.83[AMR][1000 genomes];0.91[ASN][1000 genomes]
rs35918322	0.87[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs3759586	0.85[ASN][1000 genomes]
rs4318144	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4374097	0.88[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4383078	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4444269	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4464019	0.82[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs4561394	0.88[ASN][1000 genomes]
rs4900583	0.87[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4900584	0.82[AMR][1000 genomes];0.92[ASN][1000 genomes]
rs4906340	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4906341	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906342	0.85[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs4906348	0.85[ASN][1000 genomes]
rs4906349	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58601596	0.85[ASN][1000 genomes]
rs61436277	0.86[ASN][1000 genomes]
rs61995761	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7145234	0.91[AMR][1000 genomes];0.82[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7154572	0.88[ASN][1000 genomes]
rs7155511	0.90[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7156832	0.88[ASN][1000 genomes]
rs7157116	0.88[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs7161125	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs72710744	0.83[ASN][1000 genomes]
rs745079	0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs8005540	0.83[EUR][1000 genomes]
rs8007489	0.85[ASN][1000 genomes]
rs8008451	0.82[ASN][1000 genomes]
rs8012775	0.87[AMR][1000 genomes];0.83[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8018214	0.84[AMR][1000 genomes];0.89[ASN][1000 genomes]
rs8020099	0.86[EUR][1000 genomes]
rs8021368	0.90[EUR][1000 genomes];0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:9 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3332028	chr14:103581471-104328811	Weak transcription Active TSS Enhancers Strong transcription Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	162 gene(s)	inside rSNPs	diseases
2	nsv832883	chr14:103927687-104120953	Genic enhancers Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	63 gene(s)	inside rSNPs	diseases
3	nsv902300	chr14:103967504-104205811	Active TSS Enhancers Bivalent Enhancer Flanking Active TSS Genic enhancers Weak transcription Strong transcription Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	83 gene(s)	inside rSNPs	diseases
4	nsv902305	chr14:103979953-104073551	Strong transcription Weak transcription Flanking Active TSS Enhancers Bivalent Enhancer Bivalent/Poised TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	43 gene(s)	inside rSNPs	diseases
5	nsv566022	chr14:104007555-104092789	Genic enhancers Flanking Active TSS Weak transcription Enhancers Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	24 gene(s)	inside rSNPs	diseases
6	nsv1052010	chr14:104061472-104216267	Weak transcription Active TSS Transcr. at gene 5' and 3' Genic enhancers Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
7	nsv542201	chr14:104061472-104216267	Weak transcription Enhancers Genic enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
8	nsv456435	chr14:104061646-104198251	Weak transcription Genic enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases
9	nsv566023	chr14:104061646-104198251	Strong transcription Enhancers Weak transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	52 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12435399	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs12435399	ZFYVE21	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104045600-104067200	Weak transcription	Primary B cells from cord blood	blood
3	chr14:104045800-104064200	Weak transcription	Hela-S3	cervix
4	chr14:104055800-104067000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
5	chr14:104055800-104073000	Weak transcription	Rectal Smooth Muscle	rectum
6	chr14:104056800-104064000	Weak transcription	A549	lung
7	chr14:104057000-104070800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
8	chr14:104057600-104064000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
9	chr14:104057600-104064200	Weak transcription	Skeletal Muscle Female	skeletal muscle
10	chr14:104057600-104064200	Weak transcription	Monocytes-CD14+_RO01746	blood
11	chr14:104057600-104064400	Weak transcription	Stomach Smooth Muscle	stomach
12	chr14:104057600-104073400	Weak transcription	Primary T cells from cord blood	blood
13	chr14:104057800-104064200	Weak transcription	Primary monocytes fromperipheralblood	blood
14	chr14:104057800-104064200	Weak transcription	Duodenum Smooth Muscle	Duodenum
15	chr14:104057800-104064200	Weak transcription	Sigmoid Colon	Sigmoid Colon
16	chr14:104057800-104064200	Weak transcription	Osteobl	bone
17	chr14:104057800-104073200	Weak transcription	Fetal Intestine Large	intestine
18	chr14:104057800-104073200	Weak transcription	Rectal Mucosa Donor 29	rectum
19	chr14:104057800-104073400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
20	chr14:104057800-104073400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
21	chr14:104058000-104073400	Weak transcription	H9 Cell Line	embryonic stem cell
22	chr14:104060000-104065000	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
23	chr14:104060200-104090200	Weak transcription	Pancreas	Pancrea
24	chr14:104060400-104065200	Strong transcription	Fetal Intestine Small	intestine
25	chr14:104060400-104071200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
26	chr14:104060800-104064200	Weak transcription	Spleen	Spleen
27	chr14:104060800-104073400	Weak transcription	Lung	lung
28	chr14:104061000-104064200	Weak transcription	NHDF-Ad	bronchial
29	chr14:104061000-104069200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
30	chr14:104061800-104064000	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
31	chr14:104061800-104064000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
32	chr14:104061800-104064200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
33	chr14:104061800-104064200	Weak transcription	Adipose Nuclei	Adipose
34	chr14:104061800-104064400	Weak transcription	Skeletal Muscle Male	skeletal muscle
35	chr14:104062000-104064000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr14:104062000-104064200	Weak transcription	Breast Myoepithelial Primary Cells	Breast
37	chr14:104062000-104064200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
38	chr14:104062000-104064200	Weak transcription	Brain Anterior Caudate	brain
39	chr14:104062000-104064200	Weak transcription	Brain Hippocampus Middle	brain
40	chr14:104062000-104064200	Weak transcription	Brain Inferior Temporal Lobe	brain
41	chr14:104062000-104064200	Weak transcription	Left Ventricle	heart
42	chr14:104062000-104064200	Weak transcription	HSMMtube	muscle
43	chr14:104062000-104064600	Weak transcription	Fetal Thymus	thymus
44	chr14:104062000-104064600	Weak transcription	Rectal Mucosa Donor 31	rectum
45	chr14:104062000-104065600	Weak transcription	Brain Cingulate Gyrus	brain
46	chr14:104062000-104073200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
47	chr14:104062000-104073400	Weak transcription	Ovary	ovary
48	chr14:104062200-104064000	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
49	chr14:104062200-104064400	Weak transcription	Brain Angular Gyrus	brain
50	chr14:104062200-104073200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived

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