Variant report

Variant	rs2317324
Chromosome Location	chr18:44628687-44628688
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 47 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:42)

rs_ID	r²[population]
rs12953864	0.96[EUR][1000 genomes]
rs12968552	0.88[EUR][1000 genomes]
rs13381713	0.87[CEU][hapmap];0.92[EUR][1000 genomes]
rs1434529	0.84[EUR][1000 genomes]
rs16954921	0.88[CEU][hapmap];0.94[EUR][1000 genomes]
rs16954999	0.92[CEU][hapmap];0.94[EUR][1000 genomes]
rs1836259	0.84[EUR][1000 genomes]
rs2289133	0.92[CEU][hapmap];0.93[EUR][1000 genomes]
rs2571002	0.93[EUR][1000 genomes]
rs2571004	0.92[CEU][hapmap];0.85[EUR][1000 genomes]
rs2571005	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2571006	0.92[CEU][hapmap];0.86[EUR][1000 genomes]
rs2571007	0.90[AFR][1000 genomes];0.85[AMR][1000 genomes];0.98[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2571008	0.93[EUR][1000 genomes]
rs2571010	0.96[EUR][1000 genomes]
rs2571014	0.96[CEU][hapmap];0.82[JPT][hapmap];0.87[EUR][1000 genomes];0.81[ASN][1000 genomes]
rs2571017	0.88[EUR][1000 genomes]
rs2576052	1.00[CEU][hapmap];1.00[YRI][hapmap];0.88[AFR][1000 genomes];0.83[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs2576057	0.93[EUR][1000 genomes]
rs2576058	0.93[EUR][1000 genomes]
rs2635051	0.93[EUR][1000 genomes]
rs2635052	0.94[EUR][1000 genomes]
rs2635054	0.96[EUR][1000 genomes]
rs2635056	0.88[EUR][1000 genomes]
rs2668758	0.92[CEU][hapmap];0.89[EUR][1000 genomes]
rs2668759	0.89[EUR][1000 genomes]
rs2668761	0.92[CEU][hapmap];0.92[EUR][1000 genomes]
rs2668762	0.92[EUR][1000 genomes];0.83[ASN][1000 genomes]
rs2668763	0.93[EUR][1000 genomes]
rs2668784	0.88[EUR][1000 genomes]
rs2684819	0.92[CEU][hapmap];0.88[EUR][1000 genomes]
rs2684833	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs2684851	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28718304	0.96[EUR][1000 genomes]
rs4986227	0.80[EUR][1000 genomes]
rs4986228	0.84[CEU][hapmap];0.80[EUR][1000 genomes]
rs55730206	0.93[EUR][1000 genomes]
rs7239323	0.90[AFR][1000 genomes];0.86[AMR][1000 genomes];0.99[EUR][1000 genomes];0.84[ASN][1000 genomes]
rs8085634	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];0.85[AFR][1000 genomes];0.99[AMR][1000 genomes];0.99[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs9953157	0.84[EUR][1000 genomes]
rs9956809	0.96[EUR][1000 genomes]
rs9961383	0.92[CEU][hapmap];0.93[EUR][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	nsv1067278	chr18:44564162-44629283	Enhancers Weak transcription ZNF genes & repeats Bivalent Enhancer Strong transcription Flanking Active TSS Active TSS	TF binding region CpG island Chromatin interactive region	4 gene(s)	inside rSNPs	diseases
5	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
rs2317324	HDHD2	cis	Muscle Skeletal	GTEx

Chromatin state (count:98 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44579800-44630200	Weak transcription	Right Ventricle	heart
2	chr18:44586800-44629600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
3	chr18:44587200-44630600	Weak transcription	Brain Anterior Caudate	brain
4	chr18:44587600-44629400	Weak transcription	Liver	Liver
5	chr18:44598200-44630000	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
6	chr18:44602200-44630000	Weak transcription	Fetal Muscle Leg	muscle
7	chr18:44603800-44630000	Weak transcription	Sigmoid Colon	Sigmoid Colon
8	chr18:44604000-44630200	Weak transcription	Adipose Nuclei	Adipose
9	chr18:44604000-44630600	Weak transcription	Brain Angular Gyrus	brain
10	chr18:44604800-44630800	Weak transcription	Brain Hippocampus Middle	brain
11	chr18:44605400-44630400	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
12	chr18:44607600-44637600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr18:44609200-44638400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
14	chr18:44611000-44630000	Weak transcription	Fetal Muscle Trunk	muscle
15	chr18:44611000-44633000	Weak transcription	Skeletal Muscle Male	skeletal muscle
16	chr18:44611400-44633000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
17	chr18:44611600-44630600	Weak transcription	Skeletal Muscle Female	skeletal muscle
18	chr18:44611600-44635600	Weak transcription	Psoas Muscle	Psoas
19	chr18:44612600-44632600	Weak transcription	Primary T helper cells PMA-I stimulated	--
20	chr18:44613800-44638200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
21	chr18:44615400-44630200	Weak transcription	Primary B cells from cord blood	blood
22	chr18:44615600-44631000	Weak transcription	Primary B cells from peripheral blood	blood
23	chr18:44617200-44635400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr18:44619400-44630800	Weak transcription	HSMM	muscle
25	chr18:44620000-44630600	Weak transcription	Spleen	Spleen
26	chr18:44620600-44629800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
27	chr18:44620600-44635000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
28	chr18:44620800-44675400	Weak transcription	A549	lung
29	chr18:44621000-44629000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
30	chr18:44621000-44630800	Weak transcription	Thymus	Thymus
31	chr18:44621200-44631000	Weak transcription	Rectal Mucosa Donor 29	rectum
32	chr18:44621200-44634800	Weak transcription	Pancreas	Pancrea
33	chr18:44621400-44630600	Weak transcription	Primary T cells fromperipheralblood	blood
34	chr18:44621400-44638600	Weak transcription	Colonic Mucosa	Colon
35	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
36	chr18:44622000-44633200	Weak transcription	Rectal Smooth Muscle	rectum
37	chr18:44622400-44632200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
38	chr18:44622400-44632400	Weak transcription	Brain Substantia Nigra	brain
39	chr18:44622400-44633000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
40	chr18:44622600-44630600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
41	chr18:44622800-44629400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
42	chr18:44623000-44630600	Weak transcription	Left Ventricle	heart
43	chr18:44623000-44637400	Weak transcription	Muscle Satellite Cultured Cells	--
44	chr18:44623200-44635200	Weak transcription	HepG2	liver
45	chr18:44623800-44635000	Weak transcription	Brain Inferior Temporal Lobe	brain
46	chr18:44624200-44630000	Weak transcription	Fetal Lung	lung
47	chr18:44624200-44634800	Weak transcription	Gastric	stomach
48	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
49	chr18:44624400-44632000	Weak transcription	Fetal Stomach	stomach
50	chr18:44624400-44637400	Weak transcription	HMEC	breast

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