Variant report

Variant	rs1048084
Chromosome Location	chr2:86002303-86002304
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85997012..86000139-chr2:86001257..86004684,4	MCF-7	breast:
2	chr2:85995337..85997377-chr2:86000338..86004148,3	K562	blood:
3	chr2:86001369..86004244-chr2:86027552..86029124,2	MCF-7	breast:
4	chr18:42806789..42809116-chr2:86000969..86003302,2	MCF-7	breast:
5	chr2:85998588..86002655-chr2:86008368..86012059,3	MCF-7	breast:

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

rSNPs within LD-proxies of this variant (count:6)

rs_ID	r²[population]
rs10172569	0.85[ASN][1000 genomes]
rs10190632	0.88[CEU][hapmap]
rs12475263	0.85[ASN][1000 genomes]
rs1914821	0.88[CEU][hapmap]
rs4832009	0.86[ASN][1000 genomes]
rs62147467	0.84[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv874469	chr2:85973618-86025251	Weak transcription Flanking Active TSS Transcr. at gene 5' and 3' Enhancers Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
2	nsv874470	chr2:85973618-86028257	Weak transcription Enhancers Flanking Active TSS Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	2 gene(s)	inside rSNPs	diseases
3	nsv874471	chr2:85976645-86021919	Flanking Active TSS Enhancers Bivalent Enhancer Weak transcription Genic enhancers Active TSS Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
4	nsv1001792	chr2:85983107-86016722	Genic enhancers Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
5	nsv535805	chr2:85983107-86016722	Weak transcription Enhancers Genic enhancers Active TSS Bivalent Enhancer Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	1 gene(s)	inside rSNPs	diseases
6	nsv535806	chr2:85990408-86007918	Enhancers Strong transcription Genic enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	1 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1048084	GNLY	cis	parietal	SCAN

Chromatin state (count:69 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85999000-86002400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
2	chr2:85999400-86003600	Weak transcription	Gastric	stomach
3	chr2:86000200-86010400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
4	chr2:86000400-86002400	Enhancers	Ovary	ovary
5	chr2:86000400-86002400	Enhancers	Rectal Smooth Muscle	rectum
6	chr2:86000400-86002600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
7	chr2:86000400-86004400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
8	chr2:86000400-86006000	Enhancers	Fetal Heart	heart
9	chr2:86000400-86008200	Enhancers	Psoas Muscle	Psoas
10	chr2:86000600-86002400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
11	chr2:86000600-86002600	Genic enhancers	Muscle Satellite Cultured Cells	--
12	chr2:86000600-86002600	Genic enhancers	Aorta	Aorta
13	chr2:86000600-86002800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
14	chr2:86000600-86003000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
15	chr2:86000600-86003600	Weak transcription	Pancreas	Pancrea
16	chr2:86000600-86009200	Enhancers	Right Atrium	heart
17	chr2:86000800-86002600	Enhancers	Brain Germinal Matrix	brain
18	chr2:86001000-86003800	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
19	chr2:86001000-86004000	Weak transcription	Duodenum Mucosa	Duodenum
20	chr2:86001000-86006800	Weak transcription	Stomach Mucosa	stomach
21	chr2:86001000-86008200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
22	chr2:86001200-86002400	Genic enhancers	Fetal Lung	lung
23	chr2:86001200-86002400	Genic enhancers	Fetal Stomach	stomach
24	chr2:86001200-86003600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr2:86001200-86004400	Weak transcription	Brain Anterior Caudate	brain
26	chr2:86001200-86004600	Weak transcription	Fetal Intestine Large	intestine
27	chr2:86001200-86012800	Weak transcription	Rectal Mucosa Donor 29	rectum
28	chr2:86001400-86003000	Enhancers	Colon Smooth Muscle	Colon
29	chr2:86001400-86004600	Weak transcription	Brain Substantia Nigra	brain
30	chr2:86001400-86023000	Weak transcription	Sigmoid Colon	Sigmoid Colon
31	chr2:86001600-86003600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr2:86001600-86005400	Strong transcription	Osteobl	bone
33	chr2:86001600-86006600	Enhancers	Left Ventricle	heart
34	chr2:86001600-86011800	Weak transcription	Breast Myoepithelial Primary Cells	Breast
35	chr2:86001600-86020000	Weak transcription	Fetal Brain Female	brain
36	chr2:86001600-86023000	Weak transcription	Rectal Mucosa Donor 31	rectum
37	chr2:86001800-86003400	Enhancers	Adipose Nuclei	Adipose
38	chr2:86001800-86004400	Weak transcription	NHLF	lung
39	chr2:86001800-86006000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
40	chr2:86001800-86014200	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
41	chr2:86002000-86002400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
42	chr2:86002000-86002400	Weak transcription	Brain Hippocampus Middle	brain
43	chr2:86002000-86002400	Weak transcription	Right Ventricle	heart
44	chr2:86002000-86002600	Weak transcription	Esophagus	oesophagus
45	chr2:86002000-86002600	Weak transcription	Fetal Intestine Small	intestine
46	chr2:86002000-86002800	Enhancers	HSMMtube	muscle
47	chr2:86002000-86003200	Weak transcription	Lung	lung
48	chr2:86002000-86004600	Weak transcription	Brain Angular Gyrus	brain
49	chr2:86002000-86004600	Weak transcription	Brain Inferior Temporal Lobe	brain
50	chr2:86002000-86005000	Weak transcription	Fetal Brain Male	brain

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