Variant report

Variant	rs2267844
Chromosome Location	chr3:48591481-48591482
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr3:48590915-48594977	A549	lung:	n/a	n/a
2	POLR2A	chr3:48588992-48602017	U87	brain:	n/a	n/a
3	POLR2A	chr3:48591152-48591775	U87	brain:	n/a	n/a
4	POLR2A	chr3:48591194-48591711	U87	brain:	n/a	n/a
5	POLR2A	chr3:48590851-48592116	Hela-S3	cervix:	n/a	n/a
6	POLR2A	chr3:48589038-48592203	U87	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr3:48580876..48582431-chr3:48589920..48591706,2	K562	blood:
2	chr3:48507478..48509735-chr3:48590066..48592443,2	MCF-7	breast:

Variant related genes	Relation type
PFKFB4	TF binding region
ENSG00000213689	Chromatin interaction

Extended variants
information (count: 7 )
Associated
traits (count: 10 )

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

rs_ID	r²[population]
rs12491849	0.89[ASW][hapmap];0.82[CEU][hapmap];0.90[CHD][hapmap];0.84[TSI][hapmap];1.00[YRI][hapmap]
rs2109181	1.00[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:5 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1008232	chr3:48517121-48702416	Transcr. at gene 5' and 3' Active TSS Genic enhancers Enhancers Strong transcription Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Weak transcription ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	50 gene(s)	inside rSNPs	diseases
2	nsv523981	chr3:48520289-48721040	Weak transcription Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Active TSS Bivalent Enhancer Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	52 gene(s)	inside rSNPs	diseases
3	nsv1004383	chr3:48543794-48649772	Weak transcription Enhancers Genic enhancers Strong transcription Transcr. at gene 5' and 3' Active TSS Flanking Active TSS Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
4	nsv834685	chr3:48565009-48745774	Strong transcription Active TSS Genic enhancers Weak transcription Enhancers Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	55 gene(s)	inside rSNPs	diseases
5	nsv876762	chr3:48591481-48731487	Strong transcription Enhancers Flanking Bivalent TSS/Enh Weak transcription Genic enhancers Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	53 gene(s)	inside rSNPs	diseases

mRNA abundance (count:10)

SNP	Gene	Cis/trans	Tissue	Source
rs2267844	ALAS1	cis	cerebellum	SCAN
rs2267844	TMA7	cis	Muscle Skeletal	GTEx
rs2267844	ABHD14A	cis	cerebellum	SCAN
rs2267844	ALAS1	cis	parietal	SCAN
rs2267844	TREX1	Cis_1M	lymphoblastoid	RTeQTL
rs2267844	C3orf18	cis	cerebellum	SCAN
rs2267844	AMT	cis	parietal	SCAN
rs2267844	CLEC3B	cis	cerebellum	SCAN
rs2267844	AMT	cis	cerebellum	SCAN
rs2267844	RP11-24C3.2	cis	Muscle Skeletal	GTEx

Chromatin state (count:101 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr3:48547600-48591600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
2	chr3:48562600-48592000	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
3	chr3:48570600-48591600	Weak transcription	Fetal Brain Male	brain
4	chr3:48573600-48592600	Weak transcription	NHDF-Ad	bronchial
5	chr3:48573600-48593400	Weak transcription	Pancreatic Islets	Pancreatic Islet
6	chr3:48576000-48594000	Weak transcription	Small Intestine	intestine
7	chr3:48576400-48591800	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
8	chr3:48577600-48591600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr3:48578000-48593400	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
10	chr3:48581000-48593600	Weak transcription	Right Atrium	heart
11	chr3:48581200-48593600	Weak transcription	Right Ventricle	heart
12	chr3:48581200-48593800	Weak transcription	Ovary	ovary
13	chr3:48581400-48591600	Weak transcription	Hela-S3	cervix
14	chr3:48581400-48592800	Weak transcription	Skeletal Muscle Female	skeletal muscle
15	chr3:48582600-48591800	Strong transcription	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
16	chr3:48583600-48591800	Strong transcription	NHEK	skin
17	chr3:48583800-48591600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
18	chr3:48584200-48593800	Weak transcription	Aorta	Aorta
19	chr3:48584800-48593600	Weak transcription	NH-A	brain
20	chr3:48585000-48591800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
21	chr3:48585000-48593400	Weak transcription	HSMM	muscle
22	chr3:48585200-48592600	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
23	chr3:48585200-48593400	Weak transcription	Muscle Satellite Cultured Cells	--
24	chr3:48585200-48593600	Weak transcription	Osteobl	bone
25	chr3:48585400-48592600	Weak transcription	A549	lung
26	chr3:48585800-48591600	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
27	chr3:48585800-48593400	Weak transcription	NHLF	lung
28	chr3:48586000-48591600	Weak transcription	H1 Cell Line	embryonic stem cell
29	chr3:48586200-48592600	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
30	chr3:48586400-48593200	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr3:48586400-48593400	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
32	chr3:48586400-48593400	Enhancers	Pancreas	Pancrea
33	chr3:48586400-48593600	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
34	chr3:48586600-48592200	Strong transcription	IMR90 fetal lung fibroblasts Cell Line	lung
35	chr3:48586600-48592600	Weak transcription	Brain Anterior Caudate	brain
36	chr3:48586600-48592800	Weak transcription	Brain Substantia Nigra	brain
37	chr3:48586600-48593400	Weak transcription	Primary T cells fromperipheralblood	blood
38	chr3:48586600-48593400	Weak transcription	Adipose Nuclei	Adipose
39	chr3:48586600-48593400	Weak transcription	Brain Angular Gyrus	brain
40	chr3:48586600-48593400	Weak transcription	Skeletal Muscle Male	skeletal muscle
41	chr3:48586800-48592600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
42	chr3:48586800-48592600	Weak transcription	Brain Hippocampus Middle	brain
43	chr3:48586800-48592600	Weak transcription	Brain Inferior Temporal Lobe	brain
44	chr3:48586800-48593200	Weak transcription	Duodenum Smooth Muscle	Duodenum
45	chr3:48587000-48591600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
46	chr3:48587000-48592600	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
47	chr3:48587000-48592800	Weak transcription	Brain Cingulate Gyrus	brain
48	chr3:48587200-48591600	Weak transcription	Spleen	Spleen
49	chr3:48587200-48593400	Weak transcription	Stomach Smooth Muscle	stomach
50	chr3:48587400-48593600	Enhancers	Placenta	Placenta

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