Variant report

Variant	rs1465821
Chromosome Location	chr2:86001255-86001256
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:85995337..85997377-chr2:86000338..86004148,3	K562	blood:
2	chr18:42806789..42809116-chr2:86000969..86003302,2	MCF-7	breast:
3	chr2:85995032..85998218-chr2:85998499..86001360,4	MCF-7	breast:
4	chr2:85998588..86002655-chr2:86008368..86012059,3	MCF-7	breast:

Extended variants
information (count: 26 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs11688843	0.97[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs12989354	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs13009725	0.90[AMR][1000 genomes];0.98[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs4832010	0.81[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs4832011	0.85[AMR][1000 genomes];0.95[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs4832012	0.96[CEU][hapmap];0.92[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs4832013	0.96[CEU][hapmap];0.92[GIH][hapmap];1.00[MEX][hapmap];0.95[TSI][hapmap];0.99[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs4832194	0.91[MEX][hapmap];0.89[TSI][hapmap];0.82[EUR][1000 genomes]
rs4832197	0.87[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs4832198	0.96[CEU][hapmap];0.87[MEX][hapmap];0.91[TSI][hapmap];0.83[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs59512984	0.88[ASN][1000 genomes]
rs67494720	0.87[AMR][1000 genomes];0.97[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs72928918	0.83[ASN][1000 genomes]
rs72928938	0.88[ASN][1000 genomes]
rs72928941	0.88[ASN][1000 genomes]
rs72928947	0.88[ASN][1000 genomes]
rs72928948	0.90[ASN][1000 genomes]
rs72928951	0.90[ASN][1000 genomes]
rs72928954	0.90[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	nsv874468	chr2:85926598-86001255	Enhancers Weak transcription Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Genic enhancers Active TSS Bivalent/Poised TSS Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
2	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
3	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
4	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
5	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
6	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
7	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
rs1465821	GNLY	cis	parietal	SCAN

Chromatin state (count:73 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:85994800-86002200	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:85995600-86002200	Enhancers	Liver	Liver
3	chr2:85995800-86001600	Enhancers	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
4	chr2:85995800-86002000	Enhancers	Fetal Brain Male	brain
5	chr2:85998000-86002000	Enhancers	Cortex derived primary cultured neurospheres	brain
6	chr2:85998600-86001400	Enhancers	Sigmoid Colon	Sigmoid Colon
7	chr2:85999000-86002200	Enhancers	Spleen	Spleen
8	chr2:85999000-86002400	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
9	chr2:85999200-86001800	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
10	chr2:85999400-86001600	Enhancers	Colonic Mucosa	Colon
11	chr2:85999400-86003600	Weak transcription	Gastric	stomach
12	chr2:85999800-86002200	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
13	chr2:86000000-86001800	Genic enhancers	Fetal Intestine Small	intestine
14	chr2:86000200-86001400	Enhancers	Brain Substantia Nigra	brain
15	chr2:86000200-86001800	Bivalent Enhancer	Placenta	Placenta
16	chr2:86000200-86001800	Enhancers	HepG2	liver
17	chr2:86000200-86002000	Enhancers	Brain Angular Gyrus	brain
18	chr2:86000200-86002000	Bivalent Enhancer	Fetal Adrenal Gland	Adrenal Gland
19	chr2:86000200-86010400	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
20	chr2:86000400-86001400	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
21	chr2:86000400-86001600	Enhancers	Rectal Mucosa Donor 31	rectum
22	chr2:86000400-86001600	Enhancers	HSMMtube	muscle
23	chr2:86000400-86002000	Enhancers	Brain Hippocampus Middle	brain
24	chr2:86000400-86002000	Genic enhancers	Right Ventricle	heart
25	chr2:86000400-86002200	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
26	chr2:86000400-86002200	Enhancers	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
27	chr2:86000400-86002200	Enhancers	Ganglion Eminence derived primary cultured neurospheres	brain
28	chr2:86000400-86002200	Genic enhancers	A549	lung
29	chr2:86000400-86002200	Enhancers	HUVEC	blood vessel
30	chr2:86000400-86002200	Enhancers	NHDF-Ad	bronchial
31	chr2:86000400-86002400	Enhancers	Ovary	ovary
32	chr2:86000400-86002400	Enhancers	Rectal Smooth Muscle	rectum
33	chr2:86000400-86002600	Genic enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
34	chr2:86000400-86004400	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
35	chr2:86000400-86006000	Enhancers	Fetal Heart	heart
36	chr2:86000400-86008200	Enhancers	Psoas Muscle	Psoas
37	chr2:86000600-86001600	Enhancers	Fetal Brain Female	brain
38	chr2:86000600-86001800	Genic enhancers	Adipose Nuclei	Adipose
39	chr2:86000600-86002000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
40	chr2:86000600-86002000	Genic enhancers	Lung	lung
41	chr2:86000600-86002200	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
42	chr2:86000600-86002200	Enhancers	Duodenum Smooth Muscle	Duodenum
43	chr2:86000600-86002200	Transcr. at gene 5' and 3'	Stomach Smooth Muscle	stomach
44	chr2:86000600-86002400	Genic enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
45	chr2:86000600-86002600	Genic enhancers	Muscle Satellite Cultured Cells	--
46	chr2:86000600-86002600	Genic enhancers	Aorta	Aorta
47	chr2:86000600-86002800	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr2:86000600-86003000	Genic enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
49	chr2:86000600-86003600	Weak transcription	Pancreas	Pancrea
50	chr2:86000600-86009200	Enhancers	Right Atrium	heart

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