Variant report

Variant	rs12890750
Chromosome Location	chr14:103860309-103860310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:13)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:13 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr14:103804940..103815889-chr14:103850459..103863829,28	K562	blood:
2	chr14:103794753..103806137-chr14:103849038..103864103,36	MCF-7	breast:
3	chr14:103851699..103854613-chr14:103856895..103861011,6	K562	blood:
4	chr14:103799041..103818802-chr14:103836567..103862153,82	K562	blood:
5	chr14:103797262..103804754-chr14:103849003..103864058,49	MCF-7	breast:
6	chr14:103850800..103853392-chr14:103855974..103862229,10	MCF-7	breast:
7	chr14:103858514..103860742-chr14:103895257..103897427,2	K562	blood:
8	chr14:103849131..103853013-chr14:103859929..103865676,7	MCF-7	breast:
9	chr14:103857465..103860376-chr14:103860397..103862103,2	K562	blood:
10	chr14:103798491..103802781-chr14:103859089..103862321,5	K562	blood:
11	chr14:103858689..103864179-chr14:103864270..103870415,8	K562	blood:
12	chr14:103857593..103860875-chr14:103861625..103865157,4	MCF-7	breast:
13	chr14:103859647..103862253-chr14:103892408..103894463,2	K562	blood:

No data

Variant related genes	Relation type
ENSG00000075413	Chromatin interaction
ENSG00000259775	Chromatin interaction
ENSG00000272533	Chromatin interaction
ENSG00000100664	Chromatin interaction

Extended variants
information (count: 80 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:74)

rs_ID	r²[population]
rs10134580	0.85[EUR][1000 genomes]
rs1013650	0.80[AMR][1000 genomes];0.88[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs10139279	0.85[EUR][1000 genomes]
rs10141120	0.85[EUR][1000 genomes]
rs10141388	0.86[EUR][1000 genomes]
rs10141433	0.84[EUR][1000 genomes]
rs10143247	0.85[EUR][1000 genomes]
rs10145793	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs10150072	0.82[EUR][1000 genomes]
rs1028613	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11621510	0.93[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11623869	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs11624367	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs11626483	0.81[EUR][1000 genomes]
rs11628213	0.85[EUR][1000 genomes]
rs11628969	0.87[EUR][1000 genomes]
rs12436759	0.80[AFR][1000 genomes]
rs12879085	0.80[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12888077	0.90[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs12889639	0.97[AFR][1000 genomes];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs12898029	0.94[AMR][1000 genomes];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17617941	0.85[EUR][1000 genomes]
rs17679475	0.90[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs1951392	0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1961600	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs1989565	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2010281	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2273700	0.85[EUR][1000 genomes]
rs2273703	0.85[EUR][1000 genomes]
rs2403180	0.87[EUR][1000 genomes]
rs28369539	0.85[EUR][1000 genomes]
rs28444993	0.85[EUR][1000 genomes]
rs28496120	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs28583452	0.86[EUR][1000 genomes]
rs28626081	0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs34216351	0.86[EUR][1000 genomes]
rs3742458	0.87[EUR][1000 genomes]
rs3783394	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs3783395	0.81[AMR][1000 genomes];0.90[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs3783402	0.83[EUR][1000 genomes]
rs3825566	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4900572	0.84[AFR][1000 genomes];0.91[AMR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs4906321	0.83[EUR][1000 genomes]
rs55859054	0.81[EUR][1000 genomes]
rs56365443	0.85[EUR][1000 genomes]
rs62006268	0.85[EUR][1000 genomes]
rs62007681	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs62007683	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007684	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007686	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs62007687	0.89[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs62007718	0.87[EUR][1000 genomes]
rs62007719	0.87[EUR][1000 genomes]
rs6575983	0.91[AFR][1000 genomes];0.94[AMR][1000 genomes];0.96[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs6575984	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7140564	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7145113	0.86[EUR][1000 genomes]
rs7146506	0.85[EUR][1000 genomes]
rs7150317	0.85[EUR][1000 genomes]
rs7152202	0.87[AMR][1000 genomes];0.93[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7154246	0.89[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7155014	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs7156150	0.83[EUR][1000 genomes]
rs7158144	0.90[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs7158822	0.80[AMR][1000 genomes];0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7160208	0.85[EUR][1000 genomes]
rs7160366	0.87[EUR][1000 genomes]
rs72708854	0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs72708874	0.90[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs72708893	0.85[EUR][1000 genomes]
rs8013101	0.85[EUR][1000 genomes]
rs8015918	0.87[EUR][1000 genomes]
rs8019578	0.82[EUR][1000 genomes]
rs9671911	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1042714	chr14:103085298-103860730	Enhancers Flanking Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
2	nsv1049747	chr14:103126148-103955984	Weak transcription Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	113 gene(s)	inside rSNPs	diseases
3	nsv534254	chr14:103470073-104023906	Bivalent Enhancer Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Strong transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	125 gene(s)	inside rSNPs	diseases
4	nsv9168	chr14:103531729-103913306	Enhancers Weak transcription Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Active TSS Genic enhancers Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
5	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
6	nsv542200	chr14:103838939-103868007	Enhancers Flanking Active TSS Active TSS Weak transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12890750	BAG5	Cis_1M	lymphoblastoid	RTeQTL
rs12890750	MARK3	cis	Thyroid	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:103853000-103861800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
2	chr14:103853200-103860600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
3	chr14:103853600-103860600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
4	chr14:103853600-103861800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
5	chr14:103853600-103864200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr14:103853800-103864400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
7	chr14:103853800-103867400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
8	chr14:103854600-103861800	Weak transcription	Aorta	Aorta
9	chr14:103854800-103860600	Weak transcription	Spleen	Spleen
10	chr14:103854800-103865200	Enhancers	Primary T cells fromperipheralblood	blood
11	chr14:103855000-103862400	Weak transcription	Placenta	Placenta
12	chr14:103855000-103868000	Weak transcription	Fetal Stomach	stomach
13	chr14:103855000-103874800	Weak transcription	Fetal Brain Male	brain
14	chr14:103855200-103860600	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr14:103855200-103861800	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
16	chr14:103855200-103861800	Weak transcription	Rectal Mucosa Donor 29	rectum
17	chr14:103855200-103864200	Weak transcription	Fetal Kidney	kidney
18	chr14:103855200-103865000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
19	chr14:103855200-103871800	Weak transcription	Brain Germinal Matrix	brain
20	chr14:103855400-103860600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:103856400-103863200	Enhancers	Primary T helper naive cells from peripheral blood	blood
22	chr14:103856400-103863800	Enhancers	Monocytes-CD14+_RO01746	blood
23	chr14:103856600-103863200	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
24	chr14:103856600-103863800	Enhancers	Primary T helper cells fromperipheralblood	blood
25	chr14:103856600-103871200	Enhancers	Primary T killer naive cells fromperipheralblood	blood
26	chr14:103856600-103871600	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
27	chr14:103856800-103863200	Enhancers	Primary neutrophils fromperipheralblood	blood
28	chr14:103856800-103863400	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
29	chr14:103857000-103862000	Enhancers	Primary T helper cells PMA-I stimulated	--
30	chr14:103857000-103862600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
31	chr14:103857000-103871000	Enhancers	Primary T helper naive cells fromperipheralblood	blood
32	chr14:103857600-103860600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
33	chr14:103857600-103860600	Weak transcription	Small Intestine	intestine
34	chr14:103857600-103863200	Enhancers	Liver	Liver
35	chr14:103858200-103862600	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr14:103858200-103863200	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
37	chr14:103858200-103863200	Enhancers	Skeletal Muscle Male	skeletal muscle
38	chr14:103858200-103863200	Enhancers	Skeletal Muscle Female	skeletal muscle
39	chr14:103858400-103863600	Enhancers	Breast Myoepithelial Primary Cells	Breast
40	chr14:103858400-103865000	Enhancers	Pancreas	Pancrea
41	chr14:103858800-103860400	Weak transcription	Cortex derived primary cultured neurospheres	brain
42	chr14:103858800-103860600	Weak transcription	Pancreatic Islets	Pancreatic Islet
43	chr14:103858800-103860600	Weak transcription	Ovary	ovary
44	chr14:103858800-103861800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
45	chr14:103858800-103861800	Weak transcription	HMEC	breast
46	chr14:103858800-103864400	Weak transcription	Gastric	stomach
47	chr14:103858800-103871400	Weak transcription	Fetal Brain Female	brain
48	chr14:103859200-103862600	Enhancers	Osteobl	bone
49	chr14:103859200-103863200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
50	chr14:103859400-103860400	Enhancers	Lung	lung

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