Variant report

Variant	rs12897511
Chromosome Location	chr14:104069002-104069003
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 68 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:59)

rs_ID	r²[population]
rs10047805	0.86[AFR][1000 genomes];0.86[ASN][1000 genomes]
rs10131067	0.81[AFR][1000 genomes]
rs1054080	0.82[ASN][1000 genomes]
rs1078756	0.92[ASN][1000 genomes]
rs11160754	0.89[ASN][1000 genomes]
rs11160756	0.81[ASN][1000 genomes]
rs11625397	0.82[ASN][1000 genomes]
rs11626589	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs11848721	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs11850979	0.87[ASN][1000 genomes]
rs12435399	0.90[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12589494	0.84[ASN][1000 genomes]
rs12879004	0.83[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2296483	0.81[ASN][1000 genomes]
rs2403203	0.84[ASN][1000 genomes]
rs28798508	0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28823639	0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs2896488	0.97[AMR][1000 genomes];0.96[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2896489	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs34258128	0.86[AMR][1000 genomes];0.92[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs35015260	0.81[ASN][1000 genomes]
rs35686878	0.83[ASN][1000 genomes]
rs35918322	0.81[ASN][1000 genomes]
rs3742465	0.86[ASN][1000 genomes]
rs3759586	0.84[AMR][1000 genomes];0.86[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4318144	0.95[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs4374097	0.94[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4383078	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4444269	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4464019	0.81[AFR][1000 genomes];0.98[AMR][1000 genomes];0.92[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs4561394	0.81[ASN][1000 genomes]
rs4900583	0.85[ASN][1000 genomes]
rs4900584	0.85[ASN][1000 genomes]
rs4900589	0.83[AFR][1000 genomes]
rs4906340	0.88[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906341	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4906342	0.93[AFR][1000 genomes];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4906348	0.84[AFR][1000 genomes];0.89[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4906349	0.80[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs4906355	0.85[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs58601596	0.92[ASN][1000 genomes]
rs61995761	0.92[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7142016	0.85[ASN][1000 genomes]
rs7145234	0.91[ASN][1000 genomes]
rs7154572	0.81[ASN][1000 genomes]
rs7155511	0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs7156832	0.80[ASN][1000 genomes]
rs7157116	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7161125	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs729437	0.86[AMR][1000 genomes];0.89[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs745079	0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs8005540	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs8007489	0.93[ASN][1000 genomes]
rs8007915	0.81[ASN][1000 genomes]
rs8008451	0.84[AFR][1000 genomes];0.88[ASN][1000 genomes]
rs8012775	0.86[ASN][1000 genomes]
rs8018214	0.81[ASN][1000 genomes]
rs8020099	0.86[AFR][1000 genomes];0.98[AMR][1000 genomes];0.96[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs8021368	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes];0.91[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs12897511	BAG5	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:35 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:104030800-104073200	Weak transcription	Small Intestine	intestine
2	chr14:104055800-104073000	Weak transcription	Rectal Smooth Muscle	rectum
3	chr14:104057000-104070800	Weak transcription	Primary hematopoietic stem cells short term culture	blood
4	chr14:104057600-104073400	Weak transcription	Primary T cells from cord blood	blood
5	chr14:104057800-104073200	Weak transcription	Fetal Intestine Large	intestine
6	chr14:104057800-104073200	Weak transcription	Rectal Mucosa Donor 29	rectum
7	chr14:104057800-104073400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
8	chr14:104057800-104073400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr14:104058000-104073400	Weak transcription	H9 Cell Line	embryonic stem cell
10	chr14:104060200-104090200	Weak transcription	Pancreas	Pancrea
11	chr14:104060400-104071200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
12	chr14:104060800-104073400	Weak transcription	Lung	lung
13	chr14:104061000-104069200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
14	chr14:104062000-104073200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
15	chr14:104062000-104073400	Weak transcription	Ovary	ovary
16	chr14:104062200-104073200	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
17	chr14:104062200-104073400	Weak transcription	Brain Germinal Matrix	brain
18	chr14:104062600-104072600	Weak transcription	Thymus	Thymus
19	chr14:104063200-104072800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
20	chr14:104064600-104073000	Weak transcription	Cortex derived primary cultured neurospheres	brain
21	chr14:104064600-104073400	Weak transcription	Brain Angular Gyrus	brain
22	chr14:104064800-104073000	Weak transcription	Fetal Muscle Leg	muscle
23	chr14:104064800-104073200	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
24	chr14:104064800-104073200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
25	chr14:104064800-104073400	Weak transcription	NHEK	skin
26	chr14:104064800-104073600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr14:104065000-104072800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
28	chr14:104065000-104073200	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
29	chr14:104065000-104073200	Weak transcription	Fetal Muscle Trunk	muscle
30	chr14:104065000-104073400	Weak transcription	Fetal Brain Female	brain
31	chr14:104065200-104069800	Weak transcription	Fetal Intestine Small	intestine
32	chr14:104065200-104071000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
33	chr14:104065200-104071600	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
34	chr14:104065200-104072000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
35	chr14:104065400-104071800	Weak transcription	Fetal Stomach	stomach

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