Variant report

Variant	rs2579518
Chromosome Location	chr2:96675259-96675260
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	chr2:96674813..96677740-chr2:96678852..96681143,2	K562	blood:
2	chr2:96673991..96676008-chr2:96873030..96875575,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000231584	Chromatin interaction
ENSG00000204685	Chromatin interaction
ENSG00000084090	Chromatin interaction

Extended variants
information (count: 26 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:8)

rs_ID	r²[population]
rs2438972	0.86[AMR][1000 genomes];0.83[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2438978	0.82[EUR][1000 genomes]
rs2579515	0.81[EUR][1000 genomes]
rs2579517	0.81[EUR][1000 genomes]
rs2579519	0.84[AFR][1000 genomes];0.95[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2692954	0.82[EUR][1000 genomes]
rs2969477	0.81[EUR][1000 genomes]
rs7423942	0.81[AMR][1000 genomes];0.93[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	esv3416818	chr2:96072529-96680708	Strong transcription Weak transcription Enhancers Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	43 gene(s)	inside rSNPs	diseases
2	nsv516044	chr2:96150959-96683378	Weak transcription Flanking Active TSS Genic enhancers Enhancers Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	38 gene(s)	inside rSNPs	diseases
3	nsv1003371	chr2:96326106-96684876	Flanking Active TSS Weak transcription Enhancers ZNF genes & repeats Strong transcription Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	diseases
4	nsv874666	chr2:96370571-96691125	Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Enhancers Active TSS Strong transcription Bivalent Enhancer Bivalent/Poised TSS Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	16 gene(s)	inside rSNPs	diseases
5	nsv1004486	chr2:96544604-96684876	Genic enhancers Enhancers Strong transcription Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
6	nsv874669	chr2:96547820-96691125	Strong transcription Weak transcription Enhancers ZNF genes & repeats Bivalent/Poised TSS Active TSS Genic enhancers Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
7	nsv818073	chr2:96554851-96683378	Enhancers Active TSS Weak transcription Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent Enhancer Transcr. at gene 5' and 3' Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
8	esv1840487	chr2:96582807-96836512	Enhancers Bivalent/Poised TSS Genic enhancers Flanking Active TSS Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	48 gene(s)	inside rSNPs	diseases
9	nsv870250	chr2:96610946-96739308	Flanking Active TSS Enhancers Active TSS Strong transcription Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	14 gene(s)	inside rSNPs	diseases
10	esv1837811	chr2:96622689-96730375	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	13 gene(s)	inside rSNPs	diseases
11	nsv874670	chr2:96637870-96693357	Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA	8 gene(s)	inside rSNPs	diseases
12	nsv874671	chr2:96637870-96727850	Active TSS Weak transcription Enhancers Flanking Active TSS Strong transcription Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
13	nsv874672	chr2:96637870-96809331	Enhancers Active TSS Strong transcription Flanking Active TSS Weak transcription Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	21 gene(s)	inside rSNPs	diseases
14	nsv874673	chr2:96647856-96825363	Enhancers Weak transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Strong transcription Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	46 gene(s)	inside rSNPs	diseases
15	nsv874674	chr2:96651163-96741944	Active TSS Weak transcription Flanking Active TSS Enhancers Genic enhancers Bivalent Enhancer Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	12 gene(s)	inside rSNPs	diseases
16	nsv820698	chr2:96663530-96675308	Enhancers Flanking Active TSS Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
17	esv1836563	chr2:96669134-96730375	Enhancers Active TSS Weak transcription Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Flanking Bivalent TSS/Enh Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases
18	esv993391	chr2:96671521-96731854	Weak transcription Enhancers Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	10 gene(s)	inside rSNPs	diseases

mRNA abundance (count:5)

SNP	Gene	Cis/trans	Tissue	Source
rs2579518	GPAT2	cis	Muscle Skeletal	GTEx
rs2579518	FAHD2CP	cis	lung	GTEx
rs2579518	ADRA2B	cis	Nerve Tibial	GTEx
rs2579518	ADRA2B	cis	Thyroid	GTEx
rs2579518	ASTL	cis	Esophagus Mucosa	GTEx

Chromatin state (count:72 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:96675000-96675400	Enhancers	iPS DF 6.9 Cell Line	embryonic stem cell
2	chr2:96675000-96675400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
3	chr2:96675000-96675600	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr2:96675000-96675600	Enhancers	Pancreas	Pancrea
5	chr2:96675200-96675400	Enhancers	H9 Cell Line	embryonic stem cell
6	chr2:96675200-96675400	Flanking Bivalent TSS/Enh	iPS-20b Cell Line	embryonic stem cell
7	chr2:96675200-96675400	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
8	chr2:96675200-96675400	Enhancers	Breast Myoepithelial Primary Cells	Breast
9	chr2:96675200-96675400	Flanking Active TSS	Primary T helper memory cells from peripheral blood 1	blood
10	chr2:96675200-96675400	Enhancers	Cortex derived primary cultured neurospheres	brain
11	chr2:96675200-96675400	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr2:96675200-96675400	Enhancers	Adipose Nuclei	Adipose
13	chr2:96675200-96675400	Enhancers	Brain Angular Gyrus	brain
14	chr2:96675200-96675400	Enhancers	Brain Cingulate Gyrus	brain
15	chr2:96675200-96675400	Enhancers	Brain Germinal Matrix	brain
16	chr2:96675200-96675400	Enhancers	Brain Hippocampus Middle	brain
17	chr2:96675200-96675400	Enhancers	Brain Inferior Temporal Lobe	brain
18	chr2:96675200-96675400	Enhancers	Colon Smooth Muscle	Colon
19	chr2:96675200-96675400	Enhancers	Duodenum Smooth Muscle	Duodenum
20	chr2:96675200-96675400	Enhancers	Fetal Brain Female	brain
21	chr2:96675200-96675400	Enhancers	Fetal Intestine Large	intestine
22	chr2:96675200-96675400	Enhancers	Fetal Intestine Small	intestine
23	chr2:96675200-96675400	Enhancers	Fetal Muscle Trunk	muscle
24	chr2:96675200-96675400	Enhancers	Fetal Muscle Leg	muscle
25	chr2:96675200-96675400	Flanking Active TSS	Rectal Smooth Muscle	rectum
26	chr2:96675200-96675400	Enhancers	Right Atrium	heart
27	chr2:96675200-96675400	Enhancers	Stomach Smooth Muscle	stomach
28	chr2:96675200-96675400	Enhancers	Dnd41	blood
29	chr2:96675200-96675600	Flanking Active TSS	H1 Cell Line	embryonic stem cell
30	chr2:96675200-96675600	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
31	chr2:96675200-96675600	Flanking Active TSS	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
32	chr2:96675200-96675600	Bivalent/Poised TSS	iPS-18 Cell Line	embryonic stem cell
33	chr2:96675200-96675600	Enhancers	Primary B cells from peripheral blood	blood
34	chr2:96675200-96675600	Enhancers	Primary hematopoietic stem cells short term culture	blood
35	chr2:96675200-96675600	Enhancers	Primary T helper naive cells fromperipheralblood	blood
36	chr2:96675200-96675600	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
37	chr2:96675200-96675600	Flanking Active TSS	Brain Anterior Caudate	brain
38	chr2:96675200-96675600	Enhancers	Brain Substantia Nigra	brain
39	chr2:96675200-96675600	Enhancers	Fetal Brain Male	brain
40	chr2:96675200-96675600	Flanking Active TSS	Fetal Kidney	kidney
41	chr2:96675200-96675600	Enhancers	Fetal Lung	lung
42	chr2:96675200-96675600	Enhancers	Fetal Stomach	stomach
43	chr2:96675200-96675600	Enhancers	Gastric	stomach
44	chr2:96675200-96675600	Enhancers	Left Ventricle	heart
45	chr2:96675200-96675600	Enhancers	Ovary	ovary
46	chr2:96675200-96675600	Enhancers	Psoas Muscle	Psoas
47	chr2:96675200-96675600	Enhancers	Rectal Mucosa Donor 29	rectum
48	chr2:96675200-96675600	Enhancers	Rectal Mucosa Donor 31	rectum
49	chr2:96675200-96675600	Enhancers	Right Ventricle	heart
50	chr2:96675200-96675600	Enhancers	Skeletal Muscle Male	skeletal muscle

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