Variant report

Variant	rs62096465
Chromosome Location	chr18:44629624-44629625
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	chr18:44623605-44630856	K562	blood:	n/a	n/a

Variant related genes	Relation type
ENSG00000267724	TF binding region

Extended variants
information (count: 65 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:61)

rs_ID	r²[population]
rs10083937	1.00[AFR][1000 genomes]
rs11082563	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs11082564	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs11872531	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11873880	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11875768	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs11876448	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12326122	0.91[AFR][1000 genomes]
rs12326221	1.00[AFR][1000 genomes]
rs12326412	1.00[AFR][1000 genomes]
rs12326457	1.00[AFR][1000 genomes]
rs12326465	0.84[AFR][1000 genomes]
rs12326600	0.83[ASN][1000 genomes]
rs12386076	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12386092	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs12386097	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs13547	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs1434528	0.81[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16948914	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16948928	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16949157	1.00[AFR][1000 genomes]
rs16949275	1.00[AFR][1000 genomes]
rs16952848	0.91[AFR][1000 genomes];0.83[ASN][1000 genomes]
rs16958432	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958440	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs16958699	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16958701	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs17784414	0.95[AFR][1000 genomes]
rs2117373	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs2289130	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs2289131	0.87[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs2289132	1.00[AFR][1000 genomes];0.85[ASN][1000 genomes]
rs28578518	1.00[AFR][1000 genomes]
rs28587821	1.00[AFR][1000 genomes]
rs3809965	1.00[AFR][1000 genomes]
rs3809966	1.00[AFR][1000 genomes]
rs4609941	0.91[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs56395942	1.00[AFR][1000 genomes];0.84[AMR][1000 genomes];0.82[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs57468764	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs57744138	1.00[AFR][1000 genomes]
rs57928699	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs58061761	1.00[AFR][1000 genomes]
rs60228288	1.00[AFR][1000 genomes];0.94[ASN][1000 genomes]
rs60422392	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs60726022	0.91[AFR][1000 genomes];0.84[AMR][1000 genomes]
rs60854219	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs61316646	1.00[AFR][1000 genomes];0.87[ASN][1000 genomes]
rs61689863	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62095459	0.95[AFR][1000 genomes];0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096462	1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096463	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096464	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096466	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs62096468	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096469	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096470	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096471	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096474	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096477	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096478	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs72907280	1.00[AFR][1000 genomes];0.84[AMR][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	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh 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	28 gene(s)	inside rSNPs	diseases
2	nsv833640	chr18:44552276-44714872	Enhancers Weak transcription Strong transcription Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	17 gene(s)	inside rSNPs	diseases
3	nsv909612	chr18:44560875-44681485	Weak transcription Strong transcription Enhancers Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	15 gene(s)	inside rSNPs	diseases
4	nsv576819	chr18:44602249-44677627	Strong transcription Weak transcription Flanking Active TSS Enhancers Active TSS 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	12 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62096465	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:111 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44579800-44630200	Weak transcription	Right Ventricle	heart
2	chr18:44587200-44630600	Weak transcription	Brain Anterior Caudate	brain
3	chr18:44598200-44630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
4	chr18:44602200-44630000	Weak transcription	Fetal Muscle Leg	muscle
5	chr18:44603800-44630000	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr18:44604000-44630200	Weak transcription	Adipose Nuclei	Adipose
7	chr18:44604000-44630600	Weak transcription	Brain Angular Gyrus	brain
8	chr18:44604800-44630800	Weak transcription	Brain Hippocampus Middle	brain
9	chr18:44605400-44630400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
10	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
11	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
12	chr18:44611000-44630000	Weak transcription	Fetal Muscle Trunk	muscle
13	chr18:44611000-44633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
14	chr18:44611400-44633000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr18:44611600-44630600	Weak transcription	Skeletal Muscle Female	skeletal muscle
16	chr18:44611600-44635600	Weak transcription	Psoas Muscle	Psoas
17	chr18:44612600-44632600	Weak transcription	Primary T helper cells PMA-I stimulated	--
18	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
19	chr18:44615400-44630200	Weak transcription	Primary B cells from cord blood	blood
20	chr18:44615600-44631000	Weak transcription	Primary B cells from peripheral blood	blood
21	chr18:44617200-44635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
22	chr18:44619400-44630800	Weak transcription	HSMM	muscle
23	chr18:44620000-44630600	Weak transcription	Spleen	Spleen
24	chr18:44620600-44629800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
25	chr18:44620600-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
26	chr18:44620800-44675400	Weak transcription	A549	lung
27	chr18:44621000-44630800	Weak transcription	Thymus	Thymus
28	chr18:44621200-44631000	Weak transcription	Rectal Mucosa Donor 29	rectum
29	chr18:44621200-44634800	Weak transcription	Pancreas	Pancrea
30	chr18:44621400-44630600	Weak transcription	Primary T cells fromperipheralblood	blood
31	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
32	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
33	chr18:44622000-44633200	Weak transcription	Rectal Smooth Muscle	rectum
34	chr18:44622400-44632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
35	chr18:44622400-44632400	Weak transcription	Brain Substantia Nigra	brain
36	chr18:44622400-44633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
37	chr18:44622600-44630600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
38	chr18:44623000-44630600	Weak transcription	Left Ventricle	heart
39	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
40	chr18:44623200-44635200	Weak transcription	HepG2	liver
41	chr18:44623800-44635000	Weak transcription	Brain Inferior Temporal Lobe	brain
42	chr18:44624200-44630000	Weak transcription	Fetal Lung	lung
43	chr18:44624200-44634800	Weak transcription	Gastric	stomach
44	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
45	chr18:44624400-44632000	Weak transcription	Fetal Stomach	stomach
46	chr18:44624400-44637400	Weak transcription	HMEC	breast
47	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
48	chr18:44624600-44635000	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
49	chr18:44625800-44630000	Weak transcription	Dnd41	blood
50	chr18:44625800-44632000	Weak transcription	Aorta	Aorta

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