Variant report

Variant	rs1078998
Chromosome Location	chr18:29228416-29228417
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 41 )
Associated
traits (count: 0)

rSNPs within LD-proxies of this variant (count:37)

rs_ID	r²[population]
rs1026122	0.83[AFR][1000 genomes];0.86[AMR][1000 genomes];0.95[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs1026123	0.91[JPT][hapmap];0.82[ASN][1000 genomes]
rs12962843	0.86[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1612691	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1621308	0.81[AFR][1000 genomes];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667262	0.84[AFR][1000 genomes];0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs1667274	0.95[CHB][hapmap];1.00[JPT][hapmap];0.84[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667275	0.81[CHB][hapmap];0.90[JPT][hapmap];0.86[ASN][1000 genomes]
rs1667276	0.95[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1667279	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1667280	0.81[CHB][hapmap];0.90[JPT][hapmap];0.89[ASN][1000 genomes]
rs1667281	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs1667283	0.89[ASN][1000 genomes]
rs1667284	0.81[CHB][hapmap];0.90[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667286	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs1667287	0.82[ASN][1000 genomes]
rs1791161	0.90[JPT][hapmap];0.81[ASN][1000 genomes]
rs1791169	1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1791171	0.85[CHB][hapmap];0.89[JPT][hapmap];0.89[ASN][1000 genomes]
rs1791181	0.90[ASN][1000 genomes]
rs1791192	0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1791193	0.80[AFR][1000 genomes];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs1791221	0.82[CHB][hapmap];0.91[JPT][hapmap];0.89[ASN][1000 genomes]
rs2595360	1.00[JPT][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs3764474	0.90[CHB][hapmap];1.00[JPT][hapmap];0.93[YRI][hapmap];0.83[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs3794878	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[YRI][hapmap];0.89[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3794882	0.80[AFR][1000 genomes];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs41447647	0.84[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4799311	0.95[CHB][hapmap];0.90[JPT][hapmap];0.93[YRI][hapmap];0.90[AFR][1000 genomes];0.98[AMR][1000 genomes];0.99[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs6506935	0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs7232056	0.85[EUR][1000 genomes]
rs7242641	0.83[AFR][1000 genomes];0.94[AMR][1000 genomes];0.95[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8097755	0.90[CHB][hapmap];1.00[JPT][hapmap];0.90[YRI][hapmap];0.83[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs895888	0.82[CHB][hapmap];0.91[JPT][hapmap];0.91[ASN][1000 genomes]
rs974676	0.89[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs974677	0.86[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs9950458	0.84[AFR][1000 genomes];0.98[AMR][1000 genomes];0.98[EUR][1000 genomes];0.98[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	nsv909519	chr18:29172865-29330214	Enhancers Active TSS Weak transcription Flanking Active TSS Genic enhancers Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	9 gene(s)	inside rSNPs	diseases
2	esv1831348	chr18:29205526-29268786	Weak transcription Enhancers Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Strong transcription ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
3	nsv1059078	chr18:29225522-29454980	Weak transcription Flanking Active TSS Enhancers Strong transcription Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases
4	nsv543675	chr18:29225522-29454980	Enhancers Weak transcription Strong transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	diseases

No data

Chromatin state (count:75 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:29202800-29235000	Weak transcription	Pancreas	Pancrea
2	chr18:29202800-29240200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
3	chr18:29204600-29238600	Weak transcription	Gastric	stomach
4	chr18:29208400-29229000	Weak transcription	Cortex derived primary cultured neurospheres	brain
5	chr18:29213800-29229000	Weak transcription	HUVEC	blood vessel
6	chr18:29214800-29228800	Weak transcription	NH-A	brain
7	chr18:29216000-29229000	Weak transcription	Placenta	Placenta
8	chr18:29218800-29232200	Weak transcription	Monocytes-CD14+_RO01746	blood
9	chr18:29219200-29240000	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
10	chr18:29219200-29252000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
11	chr18:29219200-29252000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:29223200-29236400	Weak transcription	Esophagus	oesophagus
13	chr18:29223600-29228800	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr18:29223800-29228800	Weak transcription	Osteobl	bone
15	chr18:29224600-29230800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr18:29224800-29228600	Enhancers	Brain Germinal Matrix	brain
17	chr18:29224800-29229200	Enhancers	HUES48 Cell Line	embryonic stem cell
18	chr18:29224800-29232400	Enhancers	Primary hematopoietic stem cells	blood
19	chr18:29225000-29229000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
20	chr18:29225200-29233600	Weak transcription	Dnd41	blood
21	chr18:29225400-29230200	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
22	chr18:29225800-29230600	Enhancers	Breast Myoepithelial Primary Cells	Breast
23	chr18:29225800-29230600	Flanking Active TSS	GM12878-XiMat	blood
24	chr18:29225800-29231600	Enhancers	HUES6 Cell Line	embryonic stem cell
25	chr18:29226000-29228600	Enhancers	iPS-15b Cell Line	embryonic stem cell
26	chr18:29226000-29229000	Enhancers	Fetal Intestine Small	intestine
27	chr18:29226000-29230600	Enhancers	ES-I3 Cell Line	embryonic stem cell
28	chr18:29226400-29228600	Enhancers	H9 Cell Line	embryonic stem cell
29	chr18:29226400-29229400	Enhancers	Fetal Adrenal Gland	Adrenal Gland
30	chr18:29226400-29230600	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
31	chr18:29226400-29230600	Enhancers	Fetal Intestine Large	intestine
32	chr18:29226600-29229200	Enhancers	iPS-18 Cell Line	embryonic stem cell
33	chr18:29226800-29229400	Enhancers	Brain Hippocampus Middle	brain
34	chr18:29226800-29231200	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
35	chr18:29226800-29232000	Weak transcription	Primary monocytes fromperipheralblood	blood
36	chr18:29227000-29230600	Enhancers	Fetal Lung	lung
37	chr18:29227400-29229200	Genic enhancers	Primary hematopoietic stem cells short term culture	blood
38	chr18:29227400-29229600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
39	chr18:29227400-29231000	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr18:29227400-29238000	Weak transcription	Rectal Mucosa Donor 29	rectum
41	chr18:29227600-29228600	Weak transcription	HUES64 Cell Line	embryonic stem cell
42	chr18:29227600-29228600	Genic enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
43	chr18:29227600-29230000	Weak transcription	Fetal Muscle Leg	muscle
44	chr18:29227600-29252000	Weak transcription	H1 Cell Line	embryonic stem cell
45	chr18:29227800-29229200	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
46	chr18:29227800-29230200	Weak transcription	Fetal Thymus	thymus
47	chr18:29227800-29230200	Weak transcription	Thymus	Thymus
48	chr18:29227800-29232400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
49	chr18:29227800-29238800	Weak transcription	Duodenum Smooth Muscle	Duodenum
50	chr18:29227800-29240800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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