Variant report

Variant	rs2016840
Chromosome Location	chr15:44211868-44211869
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	GATA3	chr15:44211808-44211955	SH-SY5Y	brain:	n/a	n/a
2	GATA2	chr15:44211680-44212103	SH-SY5Y	brain:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44209238..44212710-chr15:44213931..44216790,3	K562	blood:

Variant related genes	Relation type
FRMD5	TF binding region
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 13 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs11070414	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs1545182	0.80[CHB][hapmap];0.85[JPT][hapmap]
rs2306674	0.85[JPT][hapmap]
rs2412823	0.95[CEU][hapmap];0.95[CHB][hapmap];0.92[CHD][hapmap];0.90[JPT][hapmap];0.83[MEX][hapmap];0.95[TSI][hapmap];0.82[AMR][1000 genomes];0.89[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs2918945	0.85[JPT][hapmap]
rs597705	0.85[JPT][hapmap]
rs638224	0.81[CHB][hapmap];0.90[JPT][hapmap]
rs920339	0.81[CHB][hapmap];0.85[JPT][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	nsv1037786	chr15:43888926-44318587	Weak transcription Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Enhancers Active TSS Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
2	nsv542370	chr15:43888926-44318587	Weak transcription Genic enhancers Flanking Active TSS Active TSS Enhancers Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	90 gene(s)	inside rSNPs	diseases
3	nsv431387	chr15:43929378-44862930	Weak transcription Strong transcription Active TSS ZNF genes & repeats Enhancers Flanking Active TSS Bivalent/Poised TSS Bivalent Enhancer Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	158 gene(s)	inside rSNPs	diseases
4	nsv931051	chr15:43988761-44833518	Strong transcription Enhancers Weak transcription Active TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	154 gene(s)	inside rSNPs	diseases
5	nsv1044435	chr15:44176103-44507403	Weak transcription Enhancers Active TSS Flanking Active TSS ZNF genes & repeats Genic enhancers Bivalent/Poised TSS Strong transcription Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region	6 gene(s)	inside rSNPs	diseases

mRNA abundance (count:8)

SNP	Gene	Cis/trans	Tissue	Source
rs2016840	TGM5	cis	Lymphoblastoid	GTEx
rs2016840	CATSPER2	cis	cerebellum	SCAN
rs2016840	TGM5	cis	lymphoblastoid	seeQTL
rs2016840	DUOX2	cis	parietal	SCAN
rs2016840	STRC	cis	multi-tissue	Pritchard
rs2016840	ZNF690	cis	multi-tissue	Pritchard
rs2016840	ADAL	cis	parietal	SCAN
rs2016840	SQRDL	cis	parietal	SCAN

Chromatin state (count:59 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
2	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
3	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
4	chr15:44206000-44213400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
5	chr15:44206600-44212000	Weak transcription	Muscle Satellite Cultured Cells	--
6	chr15:44206800-44212000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
7	chr15:44206800-44212000	Weak transcription	NHDF-Ad	bronchial
8	chr15:44206800-44217800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
9	chr15:44207000-44212200	Weak transcription	Osteobl	bone
10	chr15:44207000-44214200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
11	chr15:44207200-44214600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
12	chr15:44208000-44217800	Weak transcription	NHLF	lung
13	chr15:44208400-44212200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
14	chr15:44208400-44212400	Weak transcription	Stomach Smooth Muscle	stomach
15	chr15:44208400-44212800	Weak transcription	Right Atrium	heart
16	chr15:44208400-44213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:44208400-44213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
18	chr15:44208400-44213000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
19	chr15:44208400-44213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
20	chr15:44208600-44212000	Weak transcription	Rectal Smooth Muscle	rectum
21	chr15:44208600-44213000	Weak transcription	Right Ventricle	heart
22	chr15:44208800-44213000	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
23	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
24	chr15:44209000-44212200	Weak transcription	Mesenchymal Stem Cell Derived Adipocyte Cultured Cells	ES cell derived
25	chr15:44209000-44214000	Weak transcription	NHEK	skin
26	chr15:44210000-44212600	Strong transcription	HMEC	breast
27	chr15:44210400-44213200	Enhancers	Fetal Brain Male	brain
28	chr15:44210800-44213200	Enhancers	Brain Inferior Temporal Lobe	brain
29	chr15:44210800-44214400	Enhancers	HSMMtube	muscle
30	chr15:44211000-44212600	Enhancers	Brain Hippocampus Middle	brain
31	chr15:44211000-44214200	Enhancers	Fetal Muscle Leg	muscle
32	chr15:44211200-44212800	Weak transcription	Brain Angular Gyrus	brain
33	chr15:44211400-44212400	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:44211400-44213400	Enhancers	Breast Myoepithelial Primary Cells	Breast
35	chr15:44211400-44213600	Enhancers	iPS-15b Cell Line	embryonic stem cell
36	chr15:44211400-44214400	Enhancers	Brain Dorsolateral Prefrontal Cortex	brain
37	chr15:44211600-44212000	Enhancers	H9 Cell Line	embryonic stem cell
38	chr15:44211600-44212000	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
39	chr15:44211600-44212200	Enhancers	HUES64 Cell Line	embryonic stem cell
40	chr15:44211600-44212400	Enhancers	Aorta	Aorta
41	chr15:44211600-44213000	Enhancers	Brain Cingulate Gyrus	brain
42	chr15:44211600-44213000	Weak transcription	NH-A	brain
43	chr15:44211600-44213400	Enhancers	ES-I3 Cell Line	embryonic stem cell
44	chr15:44211600-44213800	Enhancers	iPS-18 Cell Line	embryonic stem cell
45	chr15:44211600-44214000	Enhancers	iPS-20b Cell Line	embryonic stem cell
46	chr15:44211600-44214200	Enhancers	H1 Cell Line	embryonic stem cell
47	chr15:44211600-44214200	Enhancers	HUES48 Cell Line	embryonic stem cell
48	chr15:44211600-44214400	Enhancers	Brain Substantia Nigra	brain
49	chr15:44211800-44212000	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
50	chr15:44211800-44212000	Enhancers	Fetal Lung	lung

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