Variant report

Variant	rs920339
Chromosome Location	chr15:44217169-44217170
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44170061..44171966-chr15:44216673..44218203,2	K562	blood:

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];0.97[EUR][1000 genomes]
rs11070414	1.00[CEU][hapmap];1.00[CHB][hapmap];0.95[JPT][hapmap];0.82[YRI][hapmap];0.86[AFR][1000 genomes];0.97[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1545182	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[YRI][hapmap];1.00[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2016837	1.00[CEU][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];0.81[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs2016840	0.81[CHB][hapmap];0.85[JPT][hapmap]
rs2306674	0.95[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs2412822	1.00[CEU][hapmap];0.95[YRI][hapmap];0.89[AFR][1000 genomes];0.86[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs2412823	0.86[CHB][hapmap];0.95[JPT][hapmap];0.81[ASN][1000 genomes]
rs28548859	0.88[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs2918945	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.86[YRI][hapmap];0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs2918946	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs4544217	0.91[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs472797	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs530074	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs563940	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs589649	0.97[AFR][1000 genomes];0.94[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs597705	1.00[CEU][hapmap];0.95[CHB][hapmap];1.00[JPT][hapmap];0.91[YRI][hapmap];0.90[AFR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs638224	1.00[CEU][hapmap];0.90[CHB][hapmap];0.95[JPT][hapmap];0.87[YRI][hapmap];0.90[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs678513	1.00[CEU][hapmap];0.91[YRI][hapmap]
rs747714	1.00[CEU][hapmap];0.88[YRI][hapmap];0.85[AFR][1000 genomes];0.94[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs8042714	1.00[CEU][hapmap];0.91[AMR][1000 genomes];0.98[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
rs920339	ADAL	cis	Thyroid	GTEx
rs920339	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs920339	ADAL	cis	Nerve Tibial	GTEx
rs920339	CKMT1A	cis	Esophagus Mucosa	GTEx
rs920339	ADAL	cis	Esophagus Muscularis	GTEx
rs920339	TGM5	cis	Lymphoblastoid	GTEx
rs920339	ADAL	cis	Artery Tibial	GTEx
rs920339	ADAL	cis	Adipose Subcutaneous	GTEx

Chromatin state (count:47 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
2	chr15:44206800-44217800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
3	chr15:44208000-44217800	Weak transcription	NHLF	lung
4	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
5	chr15:44211800-44221800	Weak transcription	Cortex derived primary cultured neurospheres	brain
6	chr15:44211800-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
7	chr15:44212400-44218000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
8	chr15:44212400-44220600	Weak transcription	Sigmoid Colon	Sigmoid Colon
9	chr15:44212400-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
10	chr15:44212600-44218000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:44213000-44217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
12	chr15:44213400-44217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
13	chr15:44213400-44217800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
14	chr15:44213400-44217800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
15	chr15:44213400-44218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
16	chr15:44213400-44221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
17	chr15:44213600-44217800	Weak transcription	HUES64 Cell Line	embryonic stem cell
18	chr15:44213600-44218000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
19	chr15:44213600-44219800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
20	chr15:44213800-44217600	Weak transcription	HUES6 Cell Line	embryonic stem cell
21	chr15:44213800-44217800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
22	chr15:44214000-44217600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
23	chr15:44214000-44221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
24	chr15:44214000-44224400	Weak transcription	Right Atrium	heart
25	chr15:44214200-44217800	Weak transcription	HUES48 Cell Line	embryonic stem cell
26	chr15:44214200-44217800	Weak transcription	Fetal Muscle Leg	muscle
27	chr15:44214200-44218000	Weak transcription	H1 Cell Line	embryonic stem cell
28	chr15:44214200-44218200	Weak transcription	H9 Cell Line	embryonic stem cell
29	chr15:44214400-44218000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
30	chr15:44214400-44224000	Weak transcription	HSMMtube	muscle
31	chr15:44214600-44217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr15:44214800-44217800	Weak transcription	HMEC	breast
33	chr15:44215000-44218000	Weak transcription	NHEK	skin
34	chr15:44215200-44218000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
35	chr15:44215800-44221400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
36	chr15:44216200-44218000	Weak transcription	Brain Cingulate Gyrus	brain
37	chr15:44216400-44217800	Weak transcription	Brain Angular Gyrus	brain
38	chr15:44216400-44217800	Weak transcription	Brain Inferior Temporal Lobe	brain
39	chr15:44216400-44217800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
40	chr15:44216400-44218600	Weak transcription	Brain Substantia Nigra	brain
41	chr15:44216400-44220600	Weak transcription	Brain Anterior Caudate	brain
42	chr15:44216600-44219800	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:44216600-44222200	Weak transcription	NH-A	brain
44	chr15:44216800-44217800	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
45	chr15:44216800-44218000	Weak transcription	Fetal Heart	heart
46	chr15:44217000-44218200	Enhancers	NHDF-Ad	bronchial
47	chr15:44217000-44218400	Weak transcription	Brain Hippocampus Middle	brain

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