Variant report

Variant	rs45580235
Chromosome Location	chr14:105359659-105359660
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr14:105359656-105359841	HepG2	liver:	n/a	n/a
2	POLR2A	chr14:105359633-105359690	ProgFib	skin:	n/a	n/a
3	POLR2A	chr14:105358817-105360627	K562	blood:	n/a	n/a
4	POLR2A	chr14:105357493-105360907	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type
1	chr14:105340925..105344300-chr14:105357578..105360032,4	MCF-7	breast:
2	chr14:105359445..105362307-chr14:105370488..105372774,2	MCF-7	breast:
3	chr14:105358507..105360165-chr14:105487372..105489405,2	K562	blood:

Variant related genes	Relation type
CEP170B	TF binding region
ENSG00000170779	Chromatin interaction
ENSG00000259067	Chromatin interaction

Extended variants
information (count: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs10147348	0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs1866824	0.94[AFR][1000 genomes];0.99[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1866825	0.93[AFR][1000 genomes];0.99[AMR][1000 genomes];0.96[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2247712	0.89[AMR][1000 genomes];0.97[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2251389	0.81[ASN][1000 genomes]
rs2289453	0.83[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2582545	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs2582548	0.81[ASN][1000 genomes]
rs2582549	0.80[ASN][1000 genomes]
rs2841244	0.88[AMR][1000 genomes];0.88[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs2841245	0.81[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs2919629	0.80[AMR][1000 genomes];0.81[ASN][1000 genomes]
rs3742939	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs59949155	0.80[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs61996002	0.82[AMR][1000 genomes]
rs61996014	0.84[AMR][1000 genomes];0.88[ASN][1000 genomes]
rs6576063	0.81[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs752265	0.95[AMR][1000 genomes];0.96[EUR][1000 genomes];0.86[ASN][1000 genomes]
rs894038	0.82[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs9788594	0.80[AMR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv530812	chr14:104775571-105364883	Genic enhancers Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Weak transcription Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	98 gene(s)	inside rSNPs	diseases
2	nsv1053591	chr14:105024558-105475931	Active TSS Enhancers Flanking Active TSS Bivalent Enhancer Strong transcription Weak transcription Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
3	nsv542224	chr14:105024558-105475931	Bivalent Enhancer Active TSS Weak transcription Strong transcription Flanking Active TSS Enhancers Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	114 gene(s)	inside rSNPs	diseases
4	nsv902389	chr14:105092479-105366499	Flanking Active TSS Enhancers Weak transcription Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	91 gene(s)	inside rSNPs	diseases
5	esv1828345	chr14:105100787-105803170	Weak transcription Enhancers Strong transcription Genic enhancers Flanking Active TSS Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
6	nsv542225	chr14:105133688-105803170	Enhancers Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	165 gene(s)	inside rSNPs	diseases
7	nsv542227	chr14:105157572-105803170	Enhancers Flanking Active TSS Genic enhancers Weak transcription Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	147 gene(s)	inside rSNPs	diseases
8	nsv902412	chr14:105238701-105361934	Weak transcription Enhancers Strong transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	53 gene(s)	inside rSNPs	diseases
9	nsv902413	chr14:105246686-105366499	Flanking Active TSS Active TSS Weak transcription Flanking Bivalent TSS/Enh Enhancers Strong transcription Bivalent Enhancer Genic enhancers Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	54 gene(s)	inside rSNPs	diseases
10	esv1840298	chr14:105274292-105366499	Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Strong transcription Enhancers Bivalent Enhancer Weak transcription Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
11	nsv902416	chr14:105277209-105366499	Weak transcription Genic enhancers Flanking Bivalent TSS/Enh Strong transcription Enhancers Flanking Active TSS Bivalent Enhancer Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	46 gene(s)	inside rSNPs	diseases
12	nsv456456	chr14:105285159-105412541	Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Weak transcription Bivalent/Poised TSS Flanking Active TSS Transcr. at gene 5' and 3' Strong transcription ZNF genes & repeats Active TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
13	nsv566099	chr14:105285159-105412541	Bivalent Enhancer Active TSS Weak transcription Genic enhancers Flanking Active TSS Strong transcription Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	38 gene(s)	inside rSNPs	diseases
14	nsv902418	chr14:105323300-105361934	Weak transcription Strong transcription Genic enhancers Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	28 gene(s)	inside rSNPs	diseases
15	nsv917106	chr14:105339195-105803170	Enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Bivalent/Poised TSS Strong transcription Genic enhancers Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	94 gene(s)	inside rSNPs	diseases
16	nsv566139	chr14:105347296-105417147	Weak transcription Strong transcription Enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Flanking Active TSS Bivalent/Poised TSS Active TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	16 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs45580235	LINC00638	cis	lung	GTEx

Chromatin state (count:78 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr14:105339600-105363000	Weak transcription	NH-A	brain
2	chr14:105340000-105363600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
3	chr14:105347400-105362400	Weak transcription	HepG2	liver
4	chr14:105348000-105362600	Weak transcription	Brain Substantia Nigra	brain
5	chr14:105350200-105361200	Weak transcription	Stomach Mucosa	stomach
6	chr14:105350600-105362000	Weak transcription	Small Intestine	intestine
7	chr14:105351000-105361800	Weak transcription	Rectal Smooth Muscle	rectum
8	chr14:105352200-105363800	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
9	chr14:105352600-105365200	Weak transcription	Fetal Lung	lung
10	chr14:105353200-105363600	Weak transcription	Osteobl	bone
11	chr14:105353600-105360400	Weak transcription	HUVEC	blood vessel
12	chr14:105354000-105369800	Weak transcription	HSMMtube	muscle
13	chr14:105354200-105360400	Weak transcription	Left Ventricle	heart
14	chr14:105354400-105361600	Weak transcription	Colon Smooth Muscle	Colon
15	chr14:105354400-105362600	Weak transcription	Brain Hippocampus Middle	brain
16	chr14:105354400-105364600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
17	chr14:105354600-105360000	Weak transcription	Muscle Satellite Cultured Cells	--
18	chr14:105354600-105360200	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr14:105354600-105361600	Weak transcription	A549	lung
20	chr14:105354600-105362000	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
21	chr14:105354600-105362200	Weak transcription	Brain Angular Gyrus	brain
22	chr14:105354600-105363600	Weak transcription	HUES6 Cell Line	embryonic stem cell
23	chr14:105354800-105360200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
24	chr14:105354800-105362200	Weak transcription	Duodenum Smooth Muscle	Duodenum
25	chr14:105354800-105365400	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr14:105355200-105361000	Weak transcription	H9 Cell Line	embryonic stem cell
27	chr14:105355200-105365200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
28	chr14:105355400-105367000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
29	chr14:105355600-105360200	Weak transcription	Rectal Mucosa Donor 29	rectum
30	chr14:105355600-105361800	Weak transcription	Adipose Nuclei	Adipose
31	chr14:105355600-105362800	Weak transcription	Brain Cingulate Gyrus	brain
32	chr14:105355600-105363600	Weak transcription	HUES48 Cell Line	embryonic stem cell
33	chr14:105355800-105360200	Weak transcription	Brain Anterior Caudate	brain
34	chr14:105355800-105360200	Weak transcription	NHEK	skin
35	chr14:105356000-105360000	Weak transcription	Pancreas	Pancrea
36	chr14:105356000-105360200	Weak transcription	Fetal Intestine Large	intestine
37	chr14:105356000-105360600	Weak transcription	Liver	Liver
38	chr14:105356000-105361800	Weak transcription	Cortex derived primary cultured neurospheres	brain
39	chr14:105356000-105361800	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
40	chr14:105356000-105361800	Weak transcription	Aorta	Aorta
41	chr14:105356000-105362400	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr14:105356000-105363400	Weak transcription	Sigmoid Colon	Sigmoid Colon
43	chr14:105356000-105363600	Weak transcription	Ovary	ovary
44	chr14:105356200-105359800	Weak transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr14:105356200-105360000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
46	chr14:105356200-105360400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
47	chr14:105356200-105360600	Weak transcription	Fetal Brain Female	brain
48	chr14:105356200-105361400	Weak transcription	Stomach Smooth Muscle	stomach
49	chr14:105356200-105362000	Weak transcription	HMEC	breast
50	chr14:105356200-105363000	Weak transcription	Rectal Mucosa Donor 31	rectum

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