Variant report

Variant	rs62195072
Chromosome Location	chr2:234260879-234260880
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:0)
CpG islands
(count:0)
Chromatin interactive
region (count:6)
LncRNA
region (count:2)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

No data

(count:6 , 50 per page) page: 1

No.	Distal block	Cell Line	Cell type
1	chr2:234257933..234260937-chr2:234261415..234264229,3	K562	blood:
2	chr2:234252596..234255070-chr2:234259544..234261790,2	MCF-7	breast:
3	chr2:234250454..234252817-chr2:234259507..234261649,2	MCF-7	breast:
4	chr2:234258654..234260896-chr2:234262665..234264444,3	MCF-7	breast:
5	chr2:234259457..234261123-chr2:234261520..234263458,2	MCF-7	breast:
6	chr2:234259434..234265610-chr2:234290886..234296562,9	MCF-7	breast:

(count:2 , 50 per page) page: 1

No.	lncRNA name	Chromosome Location	lncRNA alias
1	lnc-USP40-1	chr2:234259778-234262062	ENSG00000259793.1
2	lnc-USP40-1	chr2:234260441-234262062	NONHSAT077479

No data

Variant related genes	Relation type
ENSG00000243637	Chromatin interaction
ENSG00000130561	Chromatin interaction
ENSG00000259793	Chromatin interaction
ENSG00000077044	Chromatin interaction

Extended variants
information (count: 12 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:5)

rs_ID	r²[population]
rs1550532	0.96[AMR][1000 genomes];0.93[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs838705	0.89[ASN][1000 genomes]
rs838708	0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs838709	0.89[AMR][1000 genomes];0.92[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs838716	0.87[AMR][1000 genomes];0.84[EUR][1000 genomes];0.81[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:7 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv584700	chr2:234199401-234364426	Enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Bivalent Enhancer Strong transcription ZNF genes & repeats Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
2	nsv1002075	chr2:234225979-234277508	Weak transcription Enhancers ZNF genes & repeats Flanking Active TSS Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
3	nsv529419	chr2:234229606-234670426	Weak transcription Enhancers Strong transcription ZNF genes & repeats Active TSS Flanking Active TSS Genic enhancers Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	39 gene(s)	inside rSNPs	diseases
4	nsv460135	chr2:234242347-234288048	Enhancers Flanking Active TSS Strong transcription Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
5	nsv584701	chr2:234242347-234288048	ZNF genes & repeats Enhancers Flanking Active TSS Strong transcription Weak transcription Genic enhancers Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv460136	chr2:234244395-234288048	Weak transcription Active TSS Enhancers Bivalent Enhancer ZNF genes & repeats Genic enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv584702	chr2:234244395-234288048	Flanking Active TSS Bivalent/Poised TSS Weak transcription Enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs62195072	DGKD	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:84 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:234255800-234262400	Weak transcription	Right Atrium	heart
2	chr2:234256400-234262400	Enhancers	Sigmoid Colon	Sigmoid Colon
3	chr2:234256600-234261400	Enhancers	Primary B cells from cord blood	blood
4	chr2:234256800-234262400	Enhancers	Primary hematopoietic stem cells short term culture	blood
5	chr2:234257000-234262200	Enhancers	Primary monocytes fromperipheralblood	blood
6	chr2:234257800-234263000	Enhancers	Placenta Amnion	Placenta Amnion
7	chr2:234258000-234261800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
8	chr2:234258200-234261200	Weak transcription	Primary T cells fromperipheralblood	blood
9	chr2:234258200-234261800	Weak transcription	Esophagus	oesophagus
10	chr2:234258200-234261800	Weak transcription	Lung	lung
11	chr2:234258200-234262000	Weak transcription	Right Ventricle	heart
12	chr2:234258200-234262600	Weak transcription	Psoas Muscle	Psoas
13	chr2:234258400-234261000	Enhancers	NHEK	skin
14	chr2:234258400-234261800	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
15	chr2:234258400-234261800	Weak transcription	Gastric	stomach
16	chr2:234258400-234261800	Weak transcription	Thymus	Thymus
17	chr2:234258400-234262000	Enhancers	Duodenum Mucosa	Duodenum
18	chr2:234258400-234262200	Enhancers	Rectal Mucosa Donor 31	rectum
19	chr2:234258400-234262400	Weak transcription	Ovary	ovary
20	chr2:234258600-234261400	Weak transcription	Primary T killer memory cells from peripheral blood	blood
21	chr2:234258600-234261800	Weak transcription	Spleen	Spleen
22	chr2:234258600-234262000	Weak transcription	Adipose Nuclei	Adipose
23	chr2:234258600-234262000	Weak transcription	Brain Substantia Nigra	brain
24	chr2:234258600-234262200	Weak transcription	Primary T cells from cord blood	blood
25	chr2:234258600-234262400	Weak transcription	Fetal Kidney	kidney
26	chr2:234258800-234262600	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
27	chr2:234259200-234261800	Weak transcription	Fetal Muscle Leg	muscle
28	chr2:234259200-234262400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
29	chr2:234259400-234261800	Weak transcription	Primary T helper cells fromperipheralblood	blood
30	chr2:234259400-234262400	Weak transcription	Brain Angular Gyrus	brain
31	chr2:234259400-234263200	Weak transcription	Small Intestine	intestine
32	chr2:234259600-234261200	Weak transcription	GM12878-XiMat	blood
33	chr2:234259600-234261600	Weak transcription	Brain Hippocampus Middle	brain
34	chr2:234259600-234261600	Weak transcription	Colonic Mucosa	Colon
35	chr2:234259600-234262200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
36	chr2:234259800-234261200	Weak transcription	Placenta	Placenta
37	chr2:234259800-234261600	Weak transcription	Skeletal Muscle Female	skeletal muscle
38	chr2:234259800-234261800	Weak transcription	Skeletal Muscle Male	skeletal muscle
39	chr2:234259800-234262000	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
40	chr2:234259800-234262000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
41	chr2:234259800-234262200	Weak transcription	Duodenum Smooth Muscle	Duodenum
42	chr2:234259800-234262400	Weak transcription	HSMMtube	muscle
43	chr2:234259800-234262400	Weak transcription	NHLF	lung
44	chr2:234260000-234261000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
45	chr2:234260000-234261000	Weak transcription	Liver	Liver
46	chr2:234260000-234261600	Weak transcription	Primary neutrophils fromperipheralblood	blood
47	chr2:234260000-234261600	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
48	chr2:234260000-234261600	Weak transcription	Stomach Mucosa	stomach
49	chr2:234260000-234261800	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:234260000-234261800	Weak transcription	Rectal Mucosa Donor 29	rectum

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