Variant report

Variant	rs62096469
Chromosome Location	chr18:44638298-44638299
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44631824..44634440-chr18:44636514..44640477,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267724	Chromatin interaction

Extended variants
information (count: 66 )
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]
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]
rs62096478	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs72907280	1.00[AFR][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
rs62096469	HDHD2	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
2	chr18:44620800-44675400	Weak transcription	A549	lung
3	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
4	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
5	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
6	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
7	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
8	chr18:44628200-44640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
9	chr18:44628600-44640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
10	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
11	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
13	chr18:44629400-44642200	Strong transcription	Liver	Liver
14	chr18:44629400-44642400	Strong transcription	Primary T cells from cord blood	blood
15	chr18:44629600-44640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
16	chr18:44629800-44642400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
17	chr18:44630000-44641600	Strong transcription	Fetal Lung	lung
18	chr18:44630000-44641800	Strong transcription	Sigmoid Colon	Sigmoid Colon
19	chr18:44630000-44641800	Strong transcription	Dnd41	blood
20	chr18:44630000-44642000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
21	chr18:44630000-44642200	Strong transcription	Duodenum Mucosa	Duodenum
22	chr18:44630000-44642600	Strong transcription	Fetal Muscle Trunk	muscle
23	chr18:44630200-44641800	Strong transcription	Adipose Nuclei	Adipose
24	chr18:44630200-44641800	Strong transcription	Duodenum Smooth Muscle	Duodenum
25	chr18:44630200-44642000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
26	chr18:44630200-44643200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
27	chr18:44630200-44646400	Strong transcription	Primary B cells from cord blood	blood
28	chr18:44630400-44641600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
29	chr18:44630400-44641800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
30	chr18:44630400-44644200	Strong transcription	Monocytes-CD14+_RO01746	blood
31	chr18:44630600-44641800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
32	chr18:44630600-44641800	Strong transcription	Left Ventricle	heart
33	chr18:44630600-44642400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
34	chr18:44630600-44642400	Strong transcription	Ovary	ovary
35	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
36	chr18:44630800-44642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
37	chr18:44630800-44642200	Strong transcription	Stomach Smooth Muscle	stomach
38	chr18:44630800-44642400	Strong transcription	Primary monocytes fromperipheralblood	blood
39	chr18:44630800-44642800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
40	chr18:44631000-44642200	Strong transcription	Primary B cells from peripheral blood	blood
41	chr18:44632000-44641800	Strong transcription	Fetal Stomach	stomach
42	chr18:44632000-44642000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
43	chr18:44632000-44654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
44	chr18:44632200-44640400	Weak transcription	K562	blood
45	chr18:44632400-44639200	Weak transcription	Primary T killer memory cells from peripheral blood	blood
46	chr18:44632400-44639200	Weak transcription	Brain Angular Gyrus	brain
47	chr18:44632400-44641800	Strong transcription	Primary neutrophils fromperipheralblood	blood
48	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
49	chr18:44632600-44641800	Strong transcription	Primary T cells fromperipheralblood	blood
50	chr18:44633000-44641600	Strong transcription	Rectal Mucosa Donor 31	rectum

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