Variant report

Variant	rs2571014
Chromosome Location	chr18:44640330-44640331
allele	C/T
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: 36 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:32)

rs_ID	r²[population]
rs12953864	0.83[EUR][1000 genomes]
rs13381713	0.83[CEU][hapmap];0.80[EUR][1000 genomes]
rs16954921	0.85[CEU][hapmap];0.82[EUR][1000 genomes]
rs16954999	0.88[CEU][hapmap];0.82[EUR][1000 genomes]
rs2289133	0.88[CEU][hapmap];0.81[EUR][1000 genomes]
rs2317324	0.96[CEU][hapmap];0.82[JPT][hapmap]
rs2571002	0.81[EUR][1000 genomes]
rs2571004	0.89[CEU][hapmap]
rs2571005	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2571006	0.89[CEU][hapmap]
rs2571007	0.89[AMR][1000 genomes];0.90[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2571008	0.86[EUR][1000 genomes]
rs2571010	0.83[EUR][1000 genomes]
rs2576052	0.96[CEU][hapmap];0.90[CHB][hapmap];0.88[AMR][1000 genomes];0.81[EUR][1000 genomes]
rs2576057	0.86[EUR][1000 genomes]
rs2576058	0.86[EUR][1000 genomes]
rs2635051	0.86[EUR][1000 genomes]
rs2635052	0.84[EUR][1000 genomes]
rs2635054	0.83[EUR][1000 genomes]
rs2668758	0.89[CEU][hapmap]
rs2668761	0.88[CEU][hapmap]
rs2668762	0.86[AMR][1000 genomes];0.81[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs2668763	0.85[EUR][1000 genomes]
rs2684819	0.89[CEU][hapmap]
rs2684833	0.96[CEU][hapmap];0.84[CHB][hapmap];1.00[YRI][hapmap];0.81[AFR][1000 genomes];0.91[AMR][1000 genomes]
rs2684851	0.87[AMR][1000 genomes];0.82[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28718304	0.83[EUR][1000 genomes]
rs55730206	0.81[EUR][1000 genomes]
rs7239323	0.90[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8085634	0.96[CEU][hapmap];0.81[JPT][hapmap];0.86[EUR][1000 genomes]
rs9956809	0.83[EUR][1000 genomes]
rs9961383	0.89[CEU][hapmap];0.81[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
rs2571014	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	chr18:44620800-44675400	Weak transcription	A549	lung
2	chr18:44621600-44674400	Weak transcription	Small Intestine	intestine
3	chr18:44624200-44654200	Weak transcription	Fetal Heart	heart
4	chr18:44624400-44640600	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
5	chr18:44626600-44664800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
6	chr18:44628600-44640600	Weak transcription	Esophagus	oesophagus
7	chr18:44628600-44641400	Weak transcription	Primary T helper naive cells from peripheral blood	blood
8	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
9	chr18:44629400-44642200	Strong transcription	Liver	Liver
10	chr18:44629400-44642400	Strong transcription	Primary T cells from cord blood	blood
11	chr18:44629600-44640400	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
12	chr18:44629800-44642400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
13	chr18:44630000-44641600	Strong transcription	Fetal Lung	lung
14	chr18:44630000-44641800	Strong transcription	Sigmoid Colon	Sigmoid Colon
15	chr18:44630000-44641800	Strong transcription	Dnd41	blood
16	chr18:44630000-44642000	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
17	chr18:44630000-44642200	Strong transcription	Duodenum Mucosa	Duodenum
18	chr18:44630000-44642600	Strong transcription	Fetal Muscle Trunk	muscle
19	chr18:44630200-44641800	Strong transcription	Adipose Nuclei	Adipose
20	chr18:44630200-44641800	Strong transcription	Duodenum Smooth Muscle	Duodenum
21	chr18:44630200-44642000	Strong transcription	Primary hematopoietic stem cells short term culture	blood
22	chr18:44630200-44643200	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
23	chr18:44630200-44646400	Strong transcription	Primary B cells from cord blood	blood
24	chr18:44630400-44641600	Strong transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
25	chr18:44630400-44641800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
26	chr18:44630400-44644200	Strong transcription	Monocytes-CD14+_RO01746	blood
27	chr18:44630600-44641800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
28	chr18:44630600-44641800	Strong transcription	Left Ventricle	heart
29	chr18:44630600-44642400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr18:44630600-44642400	Strong transcription	Ovary	ovary
31	chr18:44630600-44660400	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
32	chr18:44630800-44642200	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
33	chr18:44630800-44642200	Strong transcription	Stomach Smooth Muscle	stomach
34	chr18:44630800-44642400	Strong transcription	Primary monocytes fromperipheralblood	blood
35	chr18:44630800-44642800	Strong transcription	Primary Natural Killer cells fromperipheralblood	blood
36	chr18:44631000-44642200	Strong transcription	Primary B cells from peripheral blood	blood
37	chr18:44632000-44641800	Strong transcription	Fetal Stomach	stomach
38	chr18:44632000-44642000	Strong transcription	Primary T regulatory cells fromperipheralblood	blood
39	chr18:44632000-44654200	Weak transcription	Pancreatic Islets	Pancreatic Islet
40	chr18:44632200-44640400	Weak transcription	K562	blood
41	chr18:44632400-44641800	Strong transcription	Primary neutrophils fromperipheralblood	blood
42	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
43	chr18:44632600-44641800	Strong transcription	Primary T cells fromperipheralblood	blood
44	chr18:44633000-44641600	Strong transcription	Rectal Mucosa Donor 31	rectum
45	chr18:44633000-44641800	Strong transcription	Primary mononuclear cells fromperipheralblood	Blood
46	chr18:44633000-44641800	Strong transcription	Fetal Intestine Large	intestine
47	chr18:44633000-44641800	Strong transcription	Placenta	Placenta
48	chr18:44633000-44641800	Strong transcription	Rectal Mucosa Donor 29	rectum
49	chr18:44633200-44640400	Weak transcription	Hela-S3	cervix
50	chr18:44633200-44642000	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin

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