Variant report

Variant	rs59992752
Chromosome Location	chr14:45381119-45381120
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:2)
CpG islands
(count:0)
Chromatin interactive
region (count:2)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:2 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	MAX	chr14:45381010-45381886	ECC-1	luminal epithelium:	n/a	n/a
2	MAX	chr14:45381033-45381730	ECC-1	luminal epithelium:	n/a	n/a

No data

(count:2 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr14:45380875..45383162-chr14:45604875..45606595,2	MCF-7	breast:
2	chr14:45380945..45382495-chr14:45429574..45431197,2	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-KLHL28-1	chr14:45380960-45381120	NR_110050
2	lnc-KLHL28-1	chr14:45380960-45381142	NONHSAT036624

No data

Variant related genes	Relation type
ENSG00000258949	TF binding region
ENSG00000187790	Chromatin interaction
ENSG00000179454	Chromatin interaction

Extended variants
information (count: 139 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:130)

rs_ID	r²[population]
rs10083439	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs10129173	0.85[EUR][1000 genomes]
rs10134071	0.82[EUR][1000 genomes]
rs10135890	0.82[EUR][1000 genomes]
rs10136008	0.80[EUR][1000 genomes]
rs10136855	0.85[EUR][1000 genomes]
rs10139998	0.85[EUR][1000 genomes]
rs10140013	0.83[EUR][1000 genomes]
rs10140049	0.85[EUR][1000 genomes]
rs10140108	0.87[EUR][1000 genomes]
rs10140222	0.82[EUR][1000 genomes]
rs10140318	0.82[EUR][1000 genomes]
rs10145092	0.82[EUR][1000 genomes]
rs10145267	0.83[EUR][1000 genomes]
rs10146395	0.82[EUR][1000 genomes]
rs10147499	0.82[EUR][1000 genomes]
rs10149484	0.85[EUR][1000 genomes]
rs10150646	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs10152101	0.87[EUR][1000 genomes]
rs1053667	0.80[EUR][1000 genomes]
rs11157423	0.87[EUR][1000 genomes]
rs11157424	0.87[EUR][1000 genomes]
rs11845088	0.85[EUR][1000 genomes]
rs11845904	0.82[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs11845956	0.82[EUR][1000 genomes]
rs11846656	0.85[EUR][1000 genomes]
rs11847039	0.89[EUR][1000 genomes]
rs11848334	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs11848799	0.87[EUR][1000 genomes]
rs11849208	0.82[EUR][1000 genomes]
rs11849583	0.85[EUR][1000 genomes]
rs11850363	0.85[EUR][1000 genomes]
rs11851218	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851357	0.89[EUR][1000 genomes]
rs11851516	0.82[AFR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11851962	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs11852210	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs12100842	0.82[EUR][1000 genomes]
rs1593279	0.89[EUR][1000 genomes]
rs17115639	0.89[EUR][1000 genomes]
rs17115646	0.89[EUR][1000 genomes]
rs17115648	0.89[EUR][1000 genomes]
rs17115652	0.89[EUR][1000 genomes]
rs17115677	1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs17115680	0.85[AFR][1000 genomes]
rs17115688	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs17115703	0.87[EUR][1000 genomes]
rs17115718	0.85[EUR][1000 genomes]
rs17115787	0.82[EUR][1000 genomes]
rs2295157	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2295158	0.98[ASN][1000 genomes]
rs2295160	0.98[ASN][1000 genomes]
rs28432035	0.89[EUR][1000 genomes]
rs28448551	0.82[EUR][1000 genomes]
rs28517769	0.85[EUR][1000 genomes]
rs28558522	0.87[EUR][1000 genomes]
rs28572336	0.82[EUR][1000 genomes]
rs28594810	0.82[EUR][1000 genomes]
rs28622413	0.82[EUR][1000 genomes]
rs28681969	0.82[EUR][1000 genomes]
rs28695721	0.87[EUR][1000 genomes]
rs28703636	0.85[EUR][1000 genomes]
rs2899960	0.85[EUR][1000 genomes]
rs3736747	0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3825629	0.85[EUR][1000 genomes]
rs56386358	0.84[AMR][1000 genomes];0.96[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs56706956	0.82[EUR][1000 genomes]
rs57129780	0.86[AFR][1000 genomes];0.87[EUR][1000 genomes]
rs57147026	0.92[AFR][1000 genomes];0.95[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs57614513	0.82[EUR][1000 genomes]
rs57694277	0.82[EUR][1000 genomes]
rs58013518	0.90[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs58338525	0.89[EUR][1000 genomes]
rs58557583	0.82[AFR][1000 genomes]
rs58920861	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs60521816	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60595870	0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60891427	0.82[EUR][1000 genomes]
rs61707578	0.82[EUR][1000 genomes]
rs6572290	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs66488071	0.85[EUR][1000 genomes]
rs66535982	0.85[EUR][1000 genomes]
rs66662385	0.87[EUR][1000 genomes]
rs67643245	0.85[EUR][1000 genomes]
rs7140739	1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7145831	0.85[EUR][1000 genomes]
rs7145870	0.87[EUR][1000 genomes]
rs7147811	0.82[EUR][1000 genomes]
rs7151557	0.87[EUR][1000 genomes]
rs7158846	0.87[EUR][1000 genomes]
rs72474137	0.96[ASN][1000 genomes]
rs73334104	0.87[AFR][1000 genomes];0.89[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs73334112	0.89[EUR][1000 genomes]
rs73334114	0.89[EUR][1000 genomes]
rs73334131	0.89[EUR][1000 genomes]
rs73334135	0.87[EUR][1000 genomes]
rs73334148	0.87[EUR][1000 genomes]
rs73334154	0.87[EUR][1000 genomes]
rs73334157	0.87[EUR][1000 genomes]
rs73334162	0.87[EUR][1000 genomes]
rs73334165	0.87[EUR][1000 genomes]
rs73334172	0.87[EUR][1000 genomes]
rs73334176	0.87[EUR][1000 genomes]
rs73334913	0.82[EUR][1000 genomes]
rs73346336	0.83[EUR][1000 genomes]
rs73346344	0.87[EUR][1000 genomes]
rs73346351	0.85[EUR][1000 genomes]
rs73346360	0.85[EUR][1000 genomes]
rs73348069	0.82[EUR][1000 genomes]
rs73348076	0.82[EUR][1000 genomes]
rs73348079	0.82[EUR][1000 genomes]
rs73348088	0.82[EUR][1000 genomes]
rs73348095	0.82[EUR][1000 genomes]
rs73348939	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73348947	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73348950	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs73348953	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73348959	0.86[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs73348966	0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs73348975	0.87[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348977	0.84[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs73348981	0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73348987	0.81[AFR][1000 genomes];0.89[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs73350201	0.85[EUR][1000 genomes]
rs73352233	0.82[EUR][1000 genomes]
rs7493246	0.85[EUR][1000 genomes]
rs7493823	0.82[EUR][1000 genomes]
rs8015453	0.82[EUR][1000 genomes]
rs8022008	0.85[EUR][1000 genomes]
rs8022608	0.82[EUR][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	nsv869289	chr14:44752382-45447415	Enhancers Genic enhancers Flanking Active TSS Strong transcription Active TSS Weak transcription 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	57 gene(s)	inside rSNPs	diseases
2	nsv901832	chr14:44847444-45415597	Active TSS Weak transcription Strong transcription Enhancers Genic enhancers Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	44 gene(s)	inside rSNPs	diseases
3	nsv995092	chr14:44973489-45393462	Enhancers Bivalent/Poised TSS Active TSS Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv1047886	chr14:45189653-45543182	Strong transcription Bivalent Enhancer Active TSS Weak transcription Flanking Active TSS Enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
5	nsv542079	chr14:45189653-45543182	Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	45 gene(s)	inside rSNPs	diseases
6	nsv901841	chr14:45198196-45719643	Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	66 gene(s)	inside rSNPs	diseases
7	nsv1053437	chr14:45232269-45424222	Weak transcription Enhancers Flanking Active TSS Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	33 gene(s)	inside rSNPs	diseases
8	esv1795667	chr14:45361680-45721052	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	61 gene(s)	inside rSNPs	diseases
9	esv1794986	chr14:45368685-45650813	Weak transcription Strong transcription ZNF genes & repeats Flanking Active TSS Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs59992752	RP11-398E10.1	cis	lung	GTEx

Chromatin state (count:62 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:45367400-45381200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr14:45367400-45381200	Weak transcription	Lung	lung
3	chr14:45367600-45381400	Weak transcription	HSMM	muscle
4	chr14:45368200-45397400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr14:45371600-45381200	Weak transcription	Pancreas	Pancrea
6	chr14:45375000-45381200	Weak transcription	NHDF-Ad	bronchial
7	chr14:45375400-45403000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
8	chr14:45380600-45381200	Enhancers	Fetal Heart	heart
9	chr14:45380600-45381200	Bivalent Enhancer	Fetal Kidney	kidney
10	chr14:45380800-45381200	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr14:45380800-45381200	Bivalent Enhancer	Rectal Mucosa Donor 29	rectum
12	chr14:45380800-45381600	Bivalent/Poised TSS	Duodenum Smooth Muscle	Duodenum
13	chr14:45380800-45382000	Active TSS	Stomach Smooth Muscle	stomach
14	chr14:45381000-45381200	Bivalent/Poised TSS	HUES6 Cell Line	embryonic stem cell
15	chr14:45381000-45381200	Enhancers	Primary hematopoietic stem cells short term culture	blood
16	chr14:45381000-45381200	Flanking Bivalent TSS/Enh	Primary T helper naive cells from peripheral blood	blood
17	chr14:45381000-45381200	Flanking Bivalent TSS/Enh	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
18	chr14:45381000-45381200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
19	chr14:45381000-45381200	Active TSS	Foreskin Fibroblast Primary Cells skin01	Skin
20	chr14:45381000-45381200	Bivalent/Poised TSS	Foreskin Fibroblast Primary Cells skin02	Skin
21	chr14:45381000-45381200	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin02	Skin
22	chr14:45381000-45381200	Active TSS	Foreskin Melanocyte Primary Cells skin03	Skin
23	chr14:45381000-45381200	Bivalent/Poised TSS	Brain Cingulate Gyrus	brain
24	chr14:45381000-45381200	Flanking Active TSS	Colon Smooth Muscle	Colon
25	chr14:45381000-45381200	Bivalent/Poised TSS	Fetal Brain Female	brain
26	chr14:45381000-45381200	Bivalent Enhancer	Fetal Stomach	stomach
27	chr14:45381000-45381200	Active TSS	Left Ventricle	heart
28	chr14:45381000-45381200	Bivalent Enhancer	Skeletal Muscle Male	skeletal muscle
29	chr14:45381000-45381200	Bivalent/Poised TSS	HUVEC	blood vessel
30	chr14:45381000-45381200	Bivalent/Poised TSS	Osteobl	bone
31	chr14:45381000-45381400	Bivalent/Poised TSS	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr14:45381000-45381400	Bivalent Enhancer	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
33	chr14:45381000-45381400	Bivalent Enhancer	Primary B cells from peripheral blood	blood
34	chr14:45381000-45381400	Bivalent Enhancer	Primary T cells fromperipheralblood	blood
35	chr14:45381000-45381400	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
36	chr14:45381000-45381400	Bivalent Enhancer	Primary T killer naive cells fromperipheralblood	blood
37	chr14:45381000-45381400	Bivalent/Poised TSS	Foreskin Keratinocyte Primary Cells skin03	Skin
38	chr14:45381000-45381400	Active TSS	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr14:45381000-45381400	Flanking Bivalent TSS/Enh	Adipose Nuclei	Adipose
40	chr14:45381000-45381400	Flanking Active TSS	Brain Substantia Nigra	brain
41	chr14:45381000-45381400	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
42	chr14:45381000-45381400	Flanking Bivalent TSS/Enh	Fetal Intestine Large	intestine
43	chr14:45381000-45381600	Bivalent Enhancer	Primary T cells effector/memory enriched fromperipheralblood	blood
44	chr14:45381000-45381600	Bivalent/Poised TSS	Brain Hippocampus Middle	brain
45	chr14:45381000-45381600	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
46	chr14:45381000-45381600	Bivalent/Poised TSS	Fetal Muscle Leg	muscle
47	chr14:45381000-45381800	Bivalent/Poised TSS	HUES64 Cell Line	embryonic stem cell
48	chr14:45381000-45381800	Flanking Bivalent TSS/Enh	Primary hematopoietic stem cells G-CSF-mobilized Male	--
49	chr14:45381000-45381800	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
50	chr14:45381000-45381800	Active TSS	Aorta	Aorta

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