Variant report

Variant	rs7239323
Chromosome Location	chr18:44636506-44636507
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 45 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:41)

rs_ID	r²[population]
rs12953864	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12968552	0.81[AMR][1000 genomes];0.87[EUR][1000 genomes]
rs13381713	0.81[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs1434529	0.83[EUR][1000 genomes]
rs16954921	0.83[CEU][hapmap];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs16954999	0.87[CEU][hapmap];0.82[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs1836259	0.83[EUR][1000 genomes]
rs2289133	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs2317324	0.95[CEU][hapmap];1.00[YRI][hapmap]
rs2571002	0.81[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2571004	0.87[CEU][hapmap];0.84[EUR][1000 genomes]
rs2571005	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2571006	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.85[EUR][1000 genomes]
rs2571007	0.98[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2571008	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2571010	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2571014	0.91[CEU][hapmap];0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571017	0.82[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2576052	0.95[CEU][hapmap];1.00[YRI][hapmap];0.95[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs2576057	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2576058	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2635051	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2635052	0.84[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2635054	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2635056	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2668758	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2668759	0.82[AMR][1000 genomes];0.88[EUR][1000 genomes]
rs2668761	0.87[CEU][hapmap];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs2668762	0.87[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2668763	0.82[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs2668784	0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2684819	0.87[CEU][hapmap];0.81[AMR][1000 genomes];0.86[EUR][1000 genomes]
rs2684833	0.95[CEU][hapmap];0.92[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs2684851	0.97[AMR][1000 genomes];0.93[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28718304	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs4986228	0.91[CEU][hapmap]
rs55730206	0.92[EUR][1000 genomes]
rs8085634	0.95[CEU][hapmap];1.00[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs9953157	0.82[AMR][1000 genomes];0.83[EUR][1000 genomes]
rs9956809	0.83[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs9961383	0.87[CEU][hapmap];0.92[EUR][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
rs7239323	HDHD2	cis	Muscle Skeletal	GTEx

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
2	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
3	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
4	chr18:44620800-44675400	Weak transcription	A549	lung
5	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
6	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
7	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
8	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
9	chr18:44624400-44637400	Weak transcription	HMEC	breast
10	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
11	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
12	chr18:44626800-44637400	Weak transcription	Placenta Amnion	Placenta Amnion
13	chr18:44627000-44636600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr18:44627200-44638000	Weak transcription	H9 Cell Line	embryonic stem cell
15	chr18:44628200-44640200	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr18:44628400-44637800	Weak transcription	GM12878-XiMat	blood
17	chr18:44628600-44640000	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
18	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
19	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr18:44629000-44637600	Weak transcription	NHDF-Ad	bronchial
21	chr18:44629200-44637800	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
22	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
23	chr18:44629400-44642200	Strong transcription	Liver	Liver
24	chr18:44629400-44642400	Strong transcription	Primary T cells from cord blood	blood
25	chr18:44629600-44640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr18:44629800-44636600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
27	chr18:44629800-44642400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr18:44630000-44641600	Strong transcription	Fetal Lung	lung
29	chr18:44630000-44641800	Strong transcription	Sigmoid Colon	Sigmoid Colon
30	chr18:44630000-44641800	Strong transcription	Dnd41	blood
31	chr18:44630000-44642000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
32	chr18:44630000-44642200	Strong transcription	Duodenum Mucosa	Duodenum
33	chr18:44630000-44642600	Strong transcription	Fetal Muscle Trunk	muscle
34	chr18:44630200-44637800	Weak transcription	Osteobl	bone
35	chr18:44630200-44641800	Strong transcription	Adipose Nuclei	Adipose
36	chr18:44630200-44641800	Strong transcription	Duodenum Smooth Muscle	Duodenum
37	chr18:44630200-44642000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
38	chr18:44630200-44643200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr18:44630200-44646400	Strong transcription	Primary B cells from cord blood	blood
40	chr18:44630400-44641600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
41	chr18:44630400-44641800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
42	chr18:44630400-44644200	Strong transcription	Monocytes-CD14+_RO01746	blood
43	chr18:44630600-44641800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
44	chr18:44630600-44641800	Strong transcription	Left Ventricle	heart
45	chr18:44630600-44642400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
46	chr18:44630600-44642400	Strong transcription	Ovary	ovary
47	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
48	chr18:44630800-44642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
49	chr18:44630800-44642200	Strong transcription	Stomach Smooth Muscle	stomach
50	chr18:44630800-44642400	Strong transcription	Primary monocytes fromperipheralblood	blood

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