Variant report

Variant	rs62096478
Chromosome Location	chr18:44662409-44662410
allele	A/G
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	CEBPB	chr18:44662155-44662448	K562	blood:	n/a	chr18:44662297-44662308 chr18:44662299-44662308
2	CEBPB	chr18:44662148-44662455	HepG2	liver:	n/a	chr18:44662297-44662308 chr18:44662299-44662308

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44660900..44663835-chr18:44675479..44677959,3	MCF-7	breast:
2	chr18:44660861..44662516-chr18:44674947..44676839,2	K562	blood:

Variant related genes	Relation type
ENSG00000267800	TF binding region
ENSG00000167220	Chromatin interaction

Extended variants
information (count: 67 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:62)

rs_ID	r²[population]
rs10083937	1.00[AFR][1000 genomes]
rs11082563	1.00[AFR][1000 genomes];0.84[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11082564	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs11872531	1.00[AFR][1000 genomes]
rs11873880	1.00[AFR][1000 genomes]
rs11875768	1.00[AFR][1000 genomes]
rs11876448	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	0.93[AMR][1000 genomes];0.93[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs12386076	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12386092	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs12386097	1.00[AFR][1000 genomes];0.96[ASN][1000 genomes]
rs13547	0.95[ASN][1000 genomes]
rs1434528	0.81[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs16948914	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16948928	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs16949157	1.00[AFR][1000 genomes]
rs16949275	1.00[AFR][1000 genomes]
rs16952848	0.91[AFR][1000 genomes];0.93[AMR][1000 genomes];0.97[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs16958432	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958440	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16958699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16958701	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs17784414	0.95[AFR][1000 genomes]
rs2117373	1.00[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs2289130	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs2289131	0.87[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs2289132	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];0.84[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];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs56395942	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs57468764	0.95[ASN][1000 genomes]
rs57744138	1.00[AFR][1000 genomes]
rs57928699	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs58061761	1.00[AFR][1000 genomes]
rs60228288	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs60422392	1.00[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs60726022	0.91[AFR][1000 genomes]
rs60854219	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs61316646	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs61689863	0.95[AFR][1000 genomes];1.00[ASN][1000 genomes]
rs62095427	0.93[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs62095459	0.95[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096462	0.95[ASN][1000 genomes]
rs62096463	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096464	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096465	1.00[AFR][1000 genomes];0.95[ASN][1000 genomes]
rs62096466	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs62096468	0.95[AFR][1000 genomes];1.00[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096469	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096470	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096471	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096474	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs62096477	1.00[AFR][1000 genomes];0.98[ASN][1000 genomes]
rs72907280	1.00[AFR][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	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
5	nsv909613	chr18:44644530-44690107	Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62096478	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:123 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
5	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
6	chr18:44636200-44670600	Weak transcription	Pancreas	Pancrea
7	chr18:44639600-44665000	Weak transcription	Colonic Mucosa	Colon
8	chr18:44639600-44666400	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
9	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
10	chr18:44641600-44670400	Weak transcription	HepG2	liver
11	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
12	chr18:44641600-44675800	Weak transcription	Lung	lung
13	chr18:44641800-44662600	Weak transcription	Brain Angular Gyrus	brain
14	chr18:44641800-44663200	Weak transcription	Esophagus	oesophagus
15	chr18:44641800-44664400	Weak transcription	H9 Cell Line	embryonic stem cell
16	chr18:44641800-44665600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
17	chr18:44641800-44674400	Weak transcription	Aorta	Aorta
18	chr18:44641800-44675200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
19	chr18:44641800-44675400	Weak transcription	Fetal Intestine Small	intestine
20	chr18:44641800-44675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr18:44641800-44675800	Weak transcription	Brain Inferior Temporal Lobe	brain
22	chr18:44642000-44664600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr18:44642000-44675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
24	chr18:44642200-44674600	Weak transcription	NHEK	skin
25	chr18:44645600-44665200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
26	chr18:44645600-44667600	Weak transcription	HSMMtube	muscle
27	chr18:44647400-44663200	Weak transcription	Gastric	stomach
28	chr18:44647800-44675800	Weak transcription	Ovary	ovary
29	chr18:44649400-44664000	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
30	chr18:44650400-44670800	Weak transcription	Right Ventricle	heart
31	chr18:44653400-44668600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr18:44654200-44663400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
33	chr18:44655200-44663600	Weak transcription	Pancreatic Islets	Pancreatic Islet
34	chr18:44655800-44670000	Weak transcription	Fetal Heart	heart
35	chr18:44656400-44675200	Weak transcription	Thymus	Thymus
36	chr18:44656800-44670400	Weak transcription	Skeletal Muscle Male	skeletal muscle
37	chr18:44656800-44675000	Weak transcription	Colon Smooth Muscle	Colon
38	chr18:44656800-44675200	Weak transcription	Sigmoid Colon	Sigmoid Colon
39	chr18:44659800-44662800	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
40	chr18:44659800-44664000	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
41	chr18:44660000-44662800	Strong transcription	Muscle Satellite Cultured Cells	--
42	chr18:44660200-44662800	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
43	chr18:44660200-44662800	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
44	chr18:44660200-44664000	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
45	chr18:44660200-44667200	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr18:44660400-44662800	Strong transcription	H1 Cell Line	embryonic stem cell
47	chr18:44660400-44662800	Strong transcription	HUES6 Cell Line	embryonic stem cell
48	chr18:44660400-44662800	Strong transcription	Primary monocytes fromperipheralblood	blood
49	chr18:44660400-44662800	Strong transcription	Primary neutrophils fromperipheralblood	blood
50	chr18:44660400-44662800	Strong transcription	Primary hematopoietic stem cells short term culture	blood

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