Variant report

Variant	rs13030884
Chromosome Location	chr2:113390000-113390001
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr2:113383343..113387238-chr2:113388797..113391596,3	MCF-7	breast:
2	chr2:113389446..113391358-chr2:113401501..113403528,2	MCF-7	breast:
3	chr2:113389533..113392236-chr2:113492953..113495168,2	K562	blood:
4	chr2:113385104..113391547-chr2:113463938..113470179,6	K562	blood:
5	chr2:113388586..113390776-chr2:113395916..113398828,2	MCF-7	breast:
6	chr2:113388214..113390218-chr2:113391409..113393753,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000237753	Chromatin interaction
ENSG00000144136	Chromatin interaction

Extended variants
information (count: 24 )
Associated
traits (count: 4 )

rSNPs within LD-proxies of this variant (count:20)

rs_ID	r²[population]
rs12987250	0.84[EUR][1000 genomes]
rs13025131	0.83[EUR][1000 genomes]
rs17586834	0.83[EUR][1000 genomes]
rs17587043	0.84[EUR][1000 genomes]
rs17587297	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs17647292	0.82[EUR][1000 genomes]
rs34015418	0.84[EUR][1000 genomes]
rs35670704	0.85[EUR][1000 genomes]
rs35995321	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36079920	0.84[AMR][1000 genomes];0.90[EUR][1000 genomes]
rs36082214	0.85[EUR][1000 genomes]
rs4405766	0.96[AMR][1000 genomes];0.99[EUR][1000 genomes]
rs58770636	0.84[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs6716749	0.97[EUR][1000 genomes]
rs6716762	0.97[EUR][1000 genomes]
rs6737981	0.83[EUR][1000 genomes]
rs71414685	0.83[EUR][1000 genomes]
rs7566777	0.83[EUR][1000 genomes]
rs7607685	0.82[EUR][1000 genomes]
rs7607817	0.83[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:4 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv458997	chr2:113313794-113431092	Flanking Active TSS Strong transcription Weak transcription Genic enhancers Enhancers Active TSS 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 miRNA target site	73 gene(s)	inside rSNPs	diseases
2	nsv582708	chr2:113313794-113431092	Strong transcription Weak transcription Enhancers Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	73 gene(s)	inside rSNPs	diseases
3	nsv470480	chr2:113373950-113429752	Flanking Active TSS Strong transcription Enhancers Weak transcription Genic enhancers Bivalent Enhancer Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	51 gene(s)	inside rSNPs	diseases
4	nsv428724	chr2:113376894-113555421	Genic enhancers Strong transcription Weak transcription Enhancers Transcr. at gene 5' and 3' Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	56 gene(s)	inside rSNPs	diseases

mRNA abundance (count:4)

SNP	Gene	Cis/trans	Tissue	Source
rs13030884	AC079922.3	cis	Muscle Skeletal	GTEx
rs13030884	AC079922.3	cis	Artery Aorta	GTEx
rs13030884	AC079922.3	cis	Heart Left Ventricle	GTEx
rs13030884	AC079922.3	cis	Artery Tibial	GTEx

Chromatin state (count:67 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr2:113384200-113392400	Enhancers	H1 Derived Mesenchymal Stem Cells	ES cell derived
2	chr2:113384600-113390000	Enhancers	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
3	chr2:113385000-113396000	Weak transcription	Colonic Mucosa	Colon
4	chr2:113385000-113402600	Weak transcription	Esophagus	oesophagus
5	chr2:113385200-113390600	Enhancers	IMR90 fetal lung fibroblasts Cell Line	lung
6	chr2:113385800-113401800	Weak transcription	Brain Hippocampus Middle	brain
7	chr2:113386600-113390000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
8	chr2:113387600-113390000	Enhancers	Primary mononuclear cells fromperipheralblood	Blood
9	chr2:113388800-113390000	Enhancers	Primary T cells effector/memory enriched fromperipheralblood	blood
10	chr2:113388800-113391400	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr2:113388800-113394800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
12	chr2:113388800-113398200	Weak transcription	Lung	lung
13	chr2:113389000-113390000	Enhancers	HSMM	muscle
14	chr2:113389000-113390600	Enhancers	Primary T regulatory cells fromperipheralblood	blood
15	chr2:113389000-113390800	Enhancers	Primary hematopoietic stem cells	blood
16	chr2:113389000-113391200	Weak transcription	Placenta Amnion	Placenta Amnion
17	chr2:113389000-113391800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
18	chr2:113389000-113395000	Enhancers	Primary T helper memory cells from peripheral blood 2	blood
19	chr2:113389000-113395000	Enhancers	Primary T helper cells fromperipheralblood	blood
20	chr2:113389200-113390000	Enhancers	Primary T helper 17 cells PMA-I stimulated	--
21	chr2:113389200-113390000	Flanking Bivalent TSS/Enh	HepG2	liver
22	chr2:113389200-113390000	Enhancers	HMEC	breast
23	chr2:113389200-113394800	Enhancers	Primary T helper memory cells from peripheral blood 1	blood
24	chr2:113389200-113394800	Enhancers	Fetal Thymus	thymus
25	chr2:113389400-113390000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
26	chr2:113389400-113390000	Enhancers	Mesenchymal Stem Cell Derived Chondrocyte Cultured Cells	embryonic stem cell
27	chr2:113389400-113390000	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
28	chr2:113389400-113390600	Enhancers	Monocytes-CD14+_RO01746	blood
29	chr2:113389400-113395000	Enhancers	Primary T cells fromperipheralblood	blood
30	chr2:113389400-113402000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
31	chr2:113389600-113390000	Enhancers	Osteobl	bone
32	chr2:113389600-113391200	Enhancers	Primary T killer memory cells from peripheral blood	blood
33	chr2:113389600-113391200	Weak transcription	Placenta	Placenta
34	chr2:113389600-113391400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
35	chr2:113389600-113392000	Enhancers	Primary T killer naive cells fromperipheralblood	blood
36	chr2:113389600-113393800	Weak transcription	Rectal Mucosa Donor 29	rectum
37	chr2:113389600-113394000	Weak transcription	Spleen	Spleen
38	chr2:113389600-113394800	Enhancers	Primary T helper cells PMA-I stimulated	--
39	chr2:113389600-113395000	Enhancers	Primary T cells from cord blood	blood
40	chr2:113389600-113402200	Weak transcription	Primary B cells from cord blood	blood
41	chr2:113389800-113390000	Enhancers	GM12878-XiMat	blood
42	chr2:113389800-113390200	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
43	chr2:113389800-113390600	Enhancers	Muscle Satellite Cultured Cells	--
44	chr2:113389800-113390600	Weak transcription	K562	blood
45	chr2:113389800-113391000	Enhancers	Dnd41	blood
46	chr2:113389800-113391200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
47	chr2:113389800-113391400	Weak transcription	HUES6 Cell Line	embryonic stem cell
48	chr2:113389800-113391600	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
49	chr2:113389800-113391800	Enhancers	Primary T helper naive cells fromperipheralblood	blood
50	chr2:113389800-113392600	Enhancers	Primary hematopoietic stem cells short term culture	blood

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