Variant report

Variant	rs2016837
Chromosome Location	chr15:44211913-44211914
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: 26 )
Associated
traits (count: 8 )

rSNPs within LD-proxies of this variant (count:21)

rs_ID	r²[population]
rs1077421	1.00[CEU][hapmap];0.84[MEX][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs11070414	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.90[MEX][hapmap];0.82[MKK][hapmap];1.00[TSI][hapmap];0.87[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11635039	1.00[CHB][hapmap];0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs1545182	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.82[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2412822	1.00[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.95[MKK][hapmap];0.95[TSI][hapmap];1.00[YRI][hapmap];0.90[AFR][1000 genomes];0.93[AMR][1000 genomes];0.95[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs28548859	0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs2918945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.89[LWK][hapmap];0.90[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.90[YRI][hapmap];0.87[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2918946	0.84[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs3087657	0.85[ASW][hapmap]
rs4544217	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs472797	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs530074	1.00[CEU][hapmap];0.97[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs563940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.84[MKK][hapmap];1.00[TSI][hapmap];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs589649	0.96[AFR][1000 genomes];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs597705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.86[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.95[TSI][hapmap];0.86[YRI][hapmap];0.87[AFR][1000 genomes];0.95[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs638224	1.00[CEU][hapmap];0.90[YRI][hapmap];0.89[AFR][1000 genomes];0.85[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs663214	0.85[ASW][hapmap]
rs678513	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.91[LWK][hapmap];1.00[MEX][hapmap];0.84[MKK][hapmap];0.86[TSI][hapmap];0.86[YRI][hapmap]
rs747714	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.82[AFR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8042714	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs920339	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]

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
rs2016837	ADAL	cis	Nerve Tibial	GTEx
rs2016837	CKMT1A	cis	Esophagus Mucosa	GTEx
rs2016837	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs2016837	ADAL	cis	Esophagus Muscularis	GTEx
rs2016837	ADAL	cis	Adipose Subcutaneous	GTEx
rs2016837	TGM5	cis	lymphoblastoid	seeQTL
rs2016837	ADAL	cis	Thyroid	GTEx
rs2016837	ADAL	cis	Artery Tibial	GTEx

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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