Variant report

Variant	rs2668762
Chromosome Location	chr18:44667871-44667872
allele	A/C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr18:44667492..44671272-chr18:44701185..44704416,3	MCF-7	breast:

Variant related genes	Relation type
ENSG00000267228	Chromatin interaction
ENSG00000134049	Chromatin interaction

Extended variants
information (count: 44 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:39)

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

Chromatin state (count:113 , 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	chr18:44629200-44675800	Weak transcription	HUVEC	blood vessel
4	chr18:44632400-44675800	Weak transcription	Stomach Mucosa	stomach
5	chr18:44636200-44670600	Weak transcription	Pancreas	Pancrea
6	chr18:44640600-44675600	Weak transcription	Placenta Amnion	Placenta Amnion
7	chr18:44641600-44670400	Weak transcription	HepG2	liver
8	chr18:44641600-44674000	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
9	chr18:44641600-44675800	Weak transcription	Lung	lung
10	chr18:44641800-44674400	Weak transcription	Aorta	Aorta
11	chr18:44641800-44675200	Weak transcription	Primary T helper naive cells from peripheral blood	blood
12	chr18:44641800-44675400	Weak transcription	Fetal Intestine Small	intestine
13	chr18:44641800-44675800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
14	chr18:44641800-44675800	Weak transcription	Brain Inferior Temporal Lobe	brain
15	chr18:44642000-44675200	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
16	chr18:44642200-44674600	Weak transcription	NHEK	skin
17	chr18:44647800-44675800	Weak transcription	Ovary	ovary
18	chr18:44650400-44670800	Weak transcription	Right Ventricle	heart
19	chr18:44653400-44668600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr18:44655800-44670000	Weak transcription	Fetal Heart	heart
21	chr18:44656400-44675200	Weak transcription	Thymus	Thymus
22	chr18:44656800-44670400	Weak transcription	Skeletal Muscle Male	skeletal muscle
23	chr18:44656800-44675000	Weak transcription	Colon Smooth Muscle	Colon
24	chr18:44656800-44675200	Weak transcription	Sigmoid Colon	Sigmoid Colon
25	chr18:44661200-44668200	Weak transcription	Psoas Muscle	Psoas
26	chr18:44661200-44675800	Weak transcription	Primary T helper memory cells from peripheral blood 1	blood
27	chr18:44661400-44673600	Weak transcription	NHLF	lung
28	chr18:44661400-44674800	Weak transcription	Brain Substantia Nigra	brain
29	chr18:44661400-44675400	Weak transcription	Primary hematopoietic stem cells	blood
30	chr18:44661400-44675600	Weak transcription	Rectal Smooth Muscle	rectum
31	chr18:44661600-44670400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr18:44661600-44674800	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
33	chr18:44661600-44675600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
34	chr18:44661600-44675800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
35	chr18:44661800-44669600	Weak transcription	Left Ventricle	heart
36	chr18:44662200-44675800	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
37	chr18:44662400-44669800	Weak transcription	Fetal Thymus	thymus
38	chr18:44662400-44672400	Weak transcription	Fetal Brain Male	brain
39	chr18:44662600-44671400	Weak transcription	Primary T helper cells PMA-I stimulated	--
40	chr18:44662600-44673800	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
41	chr18:44662600-44675200	Weak transcription	Hela-S3	cervix
42	chr18:44662800-44670000	Weak transcription	K562	blood
43	chr18:44662800-44673800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
44	chr18:44662800-44674800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
45	chr18:44662800-44674800	Weak transcription	Adipose Nuclei	Adipose
46	chr18:44662800-44675000	Weak transcription	Primary hematopoietic stem cells short term culture	blood
47	chr18:44662800-44675200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
48	chr18:44662800-44675200	Weak transcription	Muscle Satellite Cultured Cells	--
49	chr18:44662800-44675400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr18:44662800-44675400	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived

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