Variant report

Variant	rs1964984
Chromosome Location	chr18:43673959-43673960
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr18:43666020..43671297-chr18:43672611..43675755,6	K562	blood:
2	chr18:43671600..43674875-chr18:43675841..43678916,7	K562	blood:
3	chr18:43673300..43675362-chr18:43687086..43690045,2	MCF-7	breast:
4	chr18:43669796..43671297-chr18:43673823..43676678,2	K562	blood:
5	chr18:43673243..43676492-chr18:43676741..43681427,5	K562	blood:

Variant related genes	Relation type
ENSG00000152234	Chromatin interaction

Extended variants
information (count: 31 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:27)

rs_ID	r²[population]
rs12709735	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs12954742	0.84[ASN][1000 genomes]
rs12966247	0.81[AMR][1000 genomes];0.80[ASN][1000 genomes]
rs1866321	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs2467669	0.81[ASN][1000 genomes]
rs2515639	0.81[ASN][1000 genomes]
rs2578183	0.87[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs2578184	0.81[ASN][1000 genomes]
rs2578187	0.81[ASN][1000 genomes]
rs2578189	0.81[ASN][1000 genomes]
rs2578192	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs2850644	0.81[ASN][1000 genomes]
rs2850646	0.88[AFR][1000 genomes];0.91[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs35935345	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3744992	0.80[ASN][1000 genomes]
rs3745002	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs3753069	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.96[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4257298	0.81[AMR][1000 genomes];0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs4275936	0.83[AMR][1000 genomes];0.83[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs6507664	0.83[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs7239525	0.92[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs7244632	0.82[ASN][1000 genomes]
rs8096719	0.80[AMR][1000 genomes]
rs9950234	0.91[AMR][1000 genomes];0.88[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9955008	0.92[AMR][1000 genomes];0.89[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs9962297	0.80[ASN][1000 genomes]
rs9965812	0.83[EUR][1000 genomes];0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1064882	chr18:43558343-43687674	Bivalent Enhancer Flanking Active TSS Enhancers Strong transcription Weak transcription Bivalent/Poised TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
2	nsv543693	chr18:43558343-43687674	Flanking Active TSS Enhancers Weak transcription Strong transcription Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	15 gene(s)	inside rSNPs	diseases
3	nsv1062024	chr18:43589516-43749410	Active TSS Strong transcription Enhancers Flanking Active TSS Weak transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv543694	chr18:43589516-43749410	Strong transcription Weak transcription Active TSS Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1964984	C18orf25	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:126 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:43657200-43674800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
2	chr18:43657200-43674800	Strong transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:43657200-43675000	Strong transcription	ES-UCSF4 Cell Line	embryonic stem cell
4	chr18:43657200-43675400	Strong transcription	HUES64 Cell Line	embryonic stem cell
5	chr18:43657200-43675400	Strong transcription	Primary hematopoietic stem cells short term culture	blood
6	chr18:43657200-43675600	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
7	chr18:43657200-43676000	Strong transcription	Osteobl	bone
8	chr18:43657200-43676200	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
9	chr18:43657400-43674600	Strong transcription	Liver	Liver
10	chr18:43657400-43674800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr18:43657400-43675000	Strong transcription	iPS-20b Cell Line	embryonic stem cell
12	chr18:43657400-43675200	Strong transcription	Monocytes-CD14+_RO01746	blood
13	chr18:43657400-43675400	Strong transcription	Placenta	Placenta
14	chr18:43657400-43675800	Strong transcription	Primary monocytes fromperipheralblood	blood
15	chr18:43657400-43675800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
16	chr18:43657600-43674400	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr18:43657600-43674600	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
18	chr18:43657600-43675200	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr18:43657800-43675200	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
20	chr18:43657800-43675800	Strong transcription	Fetal Muscle Leg	muscle
21	chr18:43657800-43676600	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
22	chr18:43658000-43675400	Strong transcription	Fetal Muscle Trunk	muscle
23	chr18:43658600-43675000	Strong transcription	iPS-18 Cell Line	embryonic stem cell
24	chr18:43658600-43675400	Strong transcription	HUES48 Cell Line	embryonic stem cell
25	chr18:43658800-43674200	Strong transcription	Duodenum Smooth Muscle	Duodenum
26	chr18:43658800-43674400	Strong transcription	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr18:43659000-43674800	Strong transcription	HUVEC	blood vessel
28	chr18:43659000-43675200	Strong transcription	Primary B cells from peripheral blood	blood
29	chr18:43659000-43675200	Strong transcription	Cortex derived primary cultured neurospheres	brain
30	chr18:43659000-43676000	Strong transcription	HUES6 Cell Line	embryonic stem cell
31	chr18:43659200-43675000	Strong transcription	Fetal Brain Female	brain
32	chr18:43659200-43675800	Strong transcription	H1 Cell Line	embryonic stem cell
33	chr18:43659400-43675800	Strong transcription	HMEC	breast
34	chr18:43659600-43674800	Strong transcription	Stomach Smooth Muscle	stomach
35	chr18:43659800-43674400	Strong transcription	Primary T helper 17 cells PMA-I stimulated	--
36	chr18:43660600-43675200	Strong transcription	Rectal Mucosa Donor 29	rectum
37	chr18:43660600-43675400	Strong transcription	Duodenum Mucosa	Duodenum
38	chr18:43661200-43675400	Strong transcription	NHEK	skin
39	chr18:43661400-43674800	Strong transcription	iPS-15b Cell Line	embryonic stem cell
40	chr18:43662600-43674000	Strong transcription	Brain Cingulate Gyrus	brain
41	chr18:43662600-43674400	Strong transcription	H9 Cell Line	embryonic stem cell
42	chr18:43662600-43674400	Strong transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
43	chr18:43662800-43674200	Strong transcription	Brain Inferior Temporal Lobe	brain
44	chr18:43662800-43674400	Strong transcription	Rectal Smooth Muscle	rectum
45	chr18:43663000-43675200	Strong transcription	NHDF-Ad	bronchial
46	chr18:43663400-43675400	Strong transcription	NH-A	brain
47	chr18:43665000-43674800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr18:43665200-43675600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
49	chr18:43668800-43674800	Strong transcription	Adipose Nuclei	Adipose
50	chr18:43669400-43675600	Strong transcription	K562	blood

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