Variant report

Variant	rs4798804
Chromosome Location	chr18:9395383-9395384
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:9393548..9395841-chr18:9396684..9399360,2	K562	blood:

Extended variants
information (count: 84 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:79)

rs_ID	r²[population]
rs1062359	0.98[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs1074159	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11081473	0.80[ASN][1000 genomes]
rs11081474	0.81[ASN][1000 genomes]
rs11663997	0.89[EUR][1000 genomes]
rs11873989	0.81[ASN][1000 genomes]
rs11876202	0.81[JPT][hapmap]
rs11878159	0.95[ASN][1000 genomes]
rs11878163	1.00[CHB][hapmap];1.00[JPT][hapmap];0.94[ASN][1000 genomes]
rs12052039	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12604438	0.80[ASN][1000 genomes]
rs12956692	0.84[CHB][hapmap]
rs12959183	0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.95[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12962014	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs12962166	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12963151	0.89[EUR][1000 genomes]
rs12967229	0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];0.98[GIH][hapmap];0.95[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.95[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs13285	0.94[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs1443599	0.81[ASN][1000 genomes]
rs1605473	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs1605474	1.00[CEU][hapmap];0.95[CHB][hapmap];0.95[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs1605476	0.92[CEU][hapmap];0.94[CHB][hapmap];0.94[JPT][hapmap];0.83[AMR][1000 genomes];0.87[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2028655	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs2048146	1.00[CHB][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs2120317	0.80[ASN][1000 genomes]
rs2298545	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.87[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2298550	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.97[ASN][1000 genomes]
rs35584133	0.93[AMR][1000 genomes];0.89[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs3786173	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs3859293	0.81[JPT][hapmap]
rs4567794	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs4797366	0.88[AMR][1000 genomes];0.87[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs4798797	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs4798801	0.97[ASN][1000 genomes]
rs4798802	1.00[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];1.00[MEX][hapmap];0.98[MKK][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs4798805	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs4798806	0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4798808	0.95[AFR][1000 genomes];0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs62087478	0.95[ASN][1000 genomes]
rs6506654	0.89[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs6506655	0.90[ASN][1000 genomes]
rs6506661	1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7228819	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7230171	0.95[ASN][1000 genomes]
rs7230328	0.95[ASN][1000 genomes]
rs7233751	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7234330	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7234762	0.85[CHB][hapmap];0.81[JPT][hapmap]
rs7236073	1.00[CHB][hapmap];0.97[CHD][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs7236396	0.95[ASN][1000 genomes]
rs7237136	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs7237485	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.91[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7239225	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7240798	0.99[AMR][1000 genomes];0.98[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs7242488	0.93[AMR][1000 genomes];0.98[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs7243376	0.95[ASN][1000 genomes]
rs7244054	0.97[ASN][1000 genomes]
rs7245034	0.82[ASW][hapmap];0.96[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72948167	0.97[ASN][1000 genomes]
rs7846	1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs8085947	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8087892	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs8093045	0.95[ASN][1000 genomes]
rs8095060	0.81[JPT][hapmap]
rs8096911	0.81[ASN][1000 genomes]
rs8097654	0.88[CHB][hapmap];0.84[JPT][hapmap];0.80[ASN][1000 genomes]
rs8097838	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8099673	0.95[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs925100	0.85[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]
rs9635819	1.00[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs965280	0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9675975	0.94[AMR][1000 genomes];0.99[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9944562	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs9956536	0.85[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9957701	0.84[CHB][hapmap];0.81[JPT][hapmap];0.81[ASN][1000 genomes]
rs9959183	0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9963516	0.87[AMR][1000 genomes];0.85[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs9966961	0.99[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs9967388	0.84[CHB][hapmap];0.81[JPT][hapmap];0.80[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv916373	chr18:9026803-9592201	Strong transcription Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	60 gene(s)	inside rSNPs	diseases
2	nsv1056407	chr18:9144345-9553764	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	42 gene(s)	inside rSNPs	diseases
3	nsv1062025	chr18:9287249-9552470	Flanking Active TSS Strong transcription Bivalent/Poised TSS Active TSS Enhancers Weak transcription ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
4	nsv543643	chr18:9287249-9552470	ZNF genes & repeats Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	35 gene(s)	inside rSNPs	diseases
5	nsv909365	chr18:9299538-9400422	Weak transcription Flanking Active TSS Strong transcription Enhancers Active TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	11 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4798804	ANKRD12	cis	parietal	SCAN
rs4798804	TWSG1	Cis_1M	lymphoblastoid	RTeQTL
rs4798804	TWSG1	cis	multi-tissue	Pritchard

Chromatin state (count:86 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:9341200-9403800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
2	chr18:9344400-9404200	Weak transcription	Primary T cells from cord blood	blood
3	chr18:9360400-9403000	Weak transcription	Primary T cells fromperipheralblood	blood
4	chr18:9364800-9409400	Weak transcription	Aorta	Aorta
5	chr18:9366600-9396200	Weak transcription	NH-A	brain
6	chr18:9366600-9406000	Weak transcription	Esophagus	oesophagus
7	chr18:9366800-9397000	Weak transcription	NHEK	skin
8	chr18:9367800-9395600	Weak transcription	Left Ventricle	heart
9	chr18:9368400-9397200	Weak transcription	Placenta	Placenta
10	chr18:9381200-9399400	Weak transcription	Colon Smooth Muscle	Colon
11	chr18:9381400-9395800	Weak transcription	Ovary	ovary
12	chr18:9381400-9404600	Weak transcription	Rectal Smooth Muscle	rectum
13	chr18:9387200-9403600	Weak transcription	K562	blood
14	chr18:9388200-9402800	Weak transcription	Sigmoid Colon	Sigmoid Colon
15	chr18:9388600-9404200	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
16	chr18:9388800-9402600	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
17	chr18:9388800-9413200	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr18:9389000-9403800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
19	chr18:9389400-9405400	Weak transcription	Lung	lung
20	chr18:9390200-9397200	Weak transcription	Small Intestine	intestine
21	chr18:9390400-9404400	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr18:9390800-9404800	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr18:9391000-9395600	Weak transcription	Fetal Stomach	stomach
24	chr18:9391000-9403800	Weak transcription	Gastric	stomach
25	chr18:9391400-9396200	Weak transcription	NHDF-Ad	bronchial
26	chr18:9391400-9404800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr18:9391600-9400200	Weak transcription	NHLF	lung
28	chr18:9392000-9395600	Weak transcription	Stomach Smooth Muscle	stomach
29	chr18:9392000-9395800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
30	chr18:9392000-9400000	Weak transcription	HUVEC	blood vessel
31	chr18:9392000-9401200	Weak transcription	Muscle Satellite Cultured Cells	--
32	chr18:9392000-9403800	Weak transcription	Monocytes-CD14+_RO01746	blood
33	chr18:9392200-9396200	Weak transcription	Duodenum Smooth Muscle	Duodenum
34	chr18:9392200-9396400	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr18:9392200-9396400	Weak transcription	Brain Anterior Caudate	brain
36	chr18:9392200-9396400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
37	chr18:9392200-9396400	Weak transcription	Osteobl	bone
38	chr18:9392200-9397200	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
39	chr18:9392200-9398000	Weak transcription	ES-I3 Cell Line	embryonic stem cell
40	chr18:9392200-9401000	Weak transcription	Brain Substantia Nigra	brain
41	chr18:9392200-9401200	Weak transcription	Fetal Intestine Large	intestine
42	chr18:9392200-9403400	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
43	chr18:9392200-9404400	Weak transcription	Adipose Nuclei	Adipose
44	chr18:9392400-9396400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
45	chr18:9392400-9396400	Weak transcription	Fetal Lung	lung
46	chr18:9392400-9398600	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
47	chr18:9392400-9400400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr18:9392400-9404600	Weak transcription	HUES64 Cell Line	embryonic stem cell
49	chr18:9392400-9404600	Weak transcription	Brain Hippocampus Middle	brain
50	chr18:9392600-9397000	Weak transcription	iPS-20b Cell Line	embryonic stem cell

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