Variant report

Variant	rs1129616
Chromosome Location	chr15:59930350-59930351
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:59923114..59927076-chr15:59929959..59933582,4	K562	blood:
2	chr15:59923114..59927076-chr15:59930243..59933582,3	K562	blood:

No.	miRNA target gene	miRNA name	Chromosome Location	mirBase accession
1	GTF2A2	hsa-miR-26b-5p	chr15:59930334-59930354

Variant related genes	Relation type
GTF2A2	miRNA target site

Extended variants
information (count: 9 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:3)

rs_ID	r²[population]
rs1871505	0.83[ASN][1000 genomes]
rs66913808	0.91[AFR][1000 genomes];0.96[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs8041223	0.85[AFR][1000 genomes];0.91[AMR][1000 genomes];0.90[EUR][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:6 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv527307	chr15:59103328-60018487	Enhancers Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Bivalent/Poised TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	145 gene(s)	inside rSNPs	diseases
2	nsv1044442	chr15:59765724-59955587	Weak transcription Enhancers Active TSS ZNF genes & repeats Strong transcription Flanking Active TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
3	nsv542403	chr15:59765724-59955587	Enhancers Weak transcription Active TSS Flanking Active TSS Bivalent Enhancer Genic enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	14 gene(s)	inside rSNPs	diseases
4	nsv569605	chr15:59855226-59956553	Strong transcription Active TSS Enhancers Weak transcription Transcr. at gene 5' and 3' Flanking Active TSS Bivalent Enhancer Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	12 gene(s)	inside rSNPs	diseases
5	nsv533240	chr15:59858093-59998176	Flanking Active TSS Strong transcription Enhancers Weak transcription Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	30 gene(s)	inside rSNPs	diseases
6	esv1824522	chr15:59919844-59987181	Weak transcription Enhancers Active TSS Strong transcription Genic enhancers Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	27 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs1129616	GTF2A2	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:118 , 50 per page) page: 1 2 3

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:59905200-59931600	Weak transcription	Fetal Stomach	stomach
2	chr15:59905200-59946200	Weak transcription	Gastric	stomach
3	chr15:59912000-59932600	Weak transcription	Colonic Mucosa	Colon
4	chr15:59912200-59935000	Weak transcription	Fetal Intestine Small	intestine
5	chr15:59914800-59937800	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
6	chr15:59920600-59947000	Weak transcription	Small Intestine	intestine
7	chr15:59925000-59936800	Weak transcription	H9 Cell Line	embryonic stem cell
8	chr15:59925000-59936800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
9	chr15:59925000-59943800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
10	chr15:59925400-59937200	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
11	chr15:59925600-59931000	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
12	chr15:59925600-59936600	Weak transcription	NHLF	lung
13	chr15:59925600-59937800	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
14	chr15:59925600-59948600	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
15	chr15:59925800-59930600	Weak transcription	K562	blood
16	chr15:59925800-59936600	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
17	chr15:59925800-59943800	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
18	chr15:59926000-59932200	Weak transcription	Rectal Smooth Muscle	rectum
19	chr15:59926200-59932600	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
20	chr15:59926200-59936800	Weak transcription	Fetal Brain Male	brain
21	chr15:59926200-59937000	Weak transcription	Placenta Amnion	Placenta Amnion
22	chr15:59926400-59935800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:59926400-59936600	Weak transcription	Brain Inferior Temporal Lobe	brain
24	chr15:59926600-59936600	Weak transcription	Brain Cingulate Gyrus	brain
25	chr15:59926600-59944000	Weak transcription	Fetal Kidney	kidney
26	chr15:59926600-59947600	Weak transcription	Right Ventricle	heart
27	chr15:59926600-59948000	Weak transcription	Brain Angular Gyrus	brain
28	chr15:59927000-59937000	Weak transcription	Lung	lung
29	chr15:59927200-59936600	Weak transcription	HMEC	breast
30	chr15:59927200-59948800	Weak transcription	Aorta	Aorta
31	chr15:59927400-59943800	Strong transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
32	chr15:59927600-59930400	Weak transcription	HUES64 Cell Line	embryonic stem cell
33	chr15:59927600-59931400	Strong transcription	Fetal Muscle Trunk	muscle
34	chr15:59927600-59933000	Strong transcription	A549	lung
35	chr15:59927600-59933800	Weak transcription	NHDF-Ad	bronchial
36	chr15:59927600-59936200	Weak transcription	Pancreas	Pancrea
37	chr15:59927800-59942800	Strong transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:59928000-59932400	Strong transcription	Fetal Muscle Leg	muscle
39	chr15:59928000-59934600	Strong transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
40	chr15:59928200-59931600	Strong transcription	Primary T cells from cord blood	blood
41	chr15:59928200-59934600	Strong transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
42	chr15:59928200-59934600	Strong transcription	Primary T helper cells PMA-I stimulated	--
43	chr15:59928400-59930400	Strong transcription	Fetal Brain Female	brain
44	chr15:59928400-59932400	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
45	chr15:59928400-59932800	Strong transcription	Left Ventricle	heart
46	chr15:59928400-59932800	Strong transcription	Stomach Smooth Muscle	stomach
47	chr15:59928400-59933600	Strong transcription	Rectal Mucosa Donor 29	rectum
48	chr15:59928400-59934400	Strong transcription	Breast Myoepithelial Primary Cells	Breast
49	chr15:59928400-59934800	Strong transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
50	chr15:59928400-59935000	Strong transcription	Primary B cells from cord blood	blood

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