Variant report

Variant	rs549433
Chromosome Location	chr12:63180816-63180817
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:62995348..62998836-chr12:63178940..63181391,3	K562	blood:
2	chr12:62995008..63000778-chr12:63178750..63184772,7	MCF-7	breast:
3	chr12:62995127..63000683-chr12:63174450..63183073,15	MCF-7	breast:

Variant related genes	Relation type
ENSG00000221949	Chromatin interaction
ENSG00000199179	Chromatin interaction
ENSG00000257354	Chromatin interaction

Extended variants
information (count: 3 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:2)

rs_ID	r²[population]
rs2704757	0.88[CHB][hapmap];0.80[CHD][hapmap];0.85[ASN][1000 genomes]
rs595455	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.82[YRI][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.99[EUR][1000 genomes];1.00[ASN][1000 genomes]

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

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv899160	chr12:63149213-63209623	Enhancers Weak transcription Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

Variant related diseases (count:1)

Disease	PMID	Source
Obesity-related traits	23251661	GWAS catalog

mRNA abundance (count:2)

SNP	Gene	Cis/trans	Tissue	Source
rs549433	AGAP2	cis	cerebellum	SCAN
rs549433	ARHGEF25	cis	parietal	SCAN

Chromatin state (count:79 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:63165600-63182000	Weak transcription	Brain Cingulate Gyrus	brain
2	chr12:63174800-63182800	Enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
3	chr12:63175200-63193600	Weak transcription	Gastric	stomach
4	chr12:63175200-63206800	Weak transcription	Pancreas	Pancrea
5	chr12:63177000-63182600	Enhancers	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
6	chr12:63177400-63181600	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
7	chr12:63177800-63181800	Enhancers	NH-A	brain
8	chr12:63178000-63185400	Weak transcription	Fetal Brain Male	brain
9	chr12:63178200-63187000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
10	chr12:63178400-63182400	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
11	chr12:63178400-63186200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
12	chr12:63178400-63192400	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr12:63178600-63186200	Weak transcription	HUES48 Cell Line	embryonic stem cell
14	chr12:63178800-63182200	Weak transcription	Brain Substantia Nigra	brain
15	chr12:63179000-63181000	Enhancers	Foreskin Keratinocyte Primary Cells skin03	Skin
16	chr12:63179200-63181600	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
17	chr12:63179200-63182200	Enhancers	ES-I3 Cell Line	embryonic stem cell
18	chr12:63179200-63182400	Enhancers	Osteobl	bone
19	chr12:63179200-63182600	Enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
20	chr12:63179400-63181000	Enhancers	Fetal Muscle Trunk	muscle
21	chr12:63179400-63181200	Enhancers	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
22	chr12:63179400-63181200	Enhancers	Primary B cells from cord blood	blood
23	chr12:63179400-63181200	Enhancers	Foreskin Keratinocyte Primary Cells skin02	Skin
24	chr12:63179400-63181600	Enhancers	Primary hematopoietic stem cells short term culture	blood
25	chr12:63179400-63181800	Enhancers	Fetal Muscle Leg	muscle
26	chr12:63179400-63182200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
27	chr12:63179400-63182200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
28	chr12:63179400-63182200	Enhancers	Fetal Adrenal Gland	Adrenal Gland
29	chr12:63179400-63182400	Enhancers	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
30	chr12:63179400-63182400	Enhancers	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
31	chr12:63179400-63182400	Enhancers	Primary neutrophils fromperipheralblood	blood
32	chr12:63179400-63182600	Strong transcription	HepG2	liver
33	chr12:63179400-63182800	Enhancers	Primary monocytes fromperipheralblood	blood
34	chr12:63179600-63181200	Enhancers	Placenta	Placenta
35	chr12:63179600-63181800	Enhancers	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
36	chr12:63179600-63181800	Enhancers	Skeletal Muscle Female	skeletal muscle
37	chr12:63179600-63182400	Enhancers	H9 Derived Neuron Cultured Cells	ES cell derived
38	chr12:63179600-63182600	Enhancers	NHDF-Ad	bronchial
39	chr12:63179600-63182800	Enhancers	Adipose Nuclei	Adipose
40	chr12:63179800-63181000	Enhancers	HUES6 Cell Line	embryonic stem cell
41	chr12:63179800-63181200	Enhancers	Spleen	Spleen
42	chr12:63179800-63181400	Genic enhancers	Brain Inferior Temporal Lobe	brain
43	chr12:63179800-63182000	Enhancers	Primary hematopoietic stem cells	blood
44	chr12:63180000-63181000	Enhancers	Right Atrium	heart
45	chr12:63180000-63181200	Enhancers	Lung	lung
46	chr12:63180000-63181200	Enhancers	Skeletal Muscle Male	skeletal muscle
47	chr12:63180000-63182000	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
48	chr12:63180000-63183000	Strong transcription	Fetal Intestine Small	intestine
49	chr12:63180000-63184200	Weak transcription	Small Intestine	intestine
50	chr12:63180200-63181000	Enhancers	HMEC	breast

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