Variant report

Variant	rs678513
Chromosome Location	chr15:44192817-44192818
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 26 )
Associated
traits (count: 8 )

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

rs_ID	r²[population]
rs1077421	1.00[CEU][hapmap];0.83[MEX][hapmap];0.82[TSI][hapmap]
rs11070414	0.86[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];0.89[MEX][hapmap];0.88[MKK][hapmap];0.86[TSI][hapmap];0.81[EUR][1000 genomes]
rs11635039	0.87[CHB][hapmap]
rs13329084	0.83[TSI][hapmap]
rs1545182	1.00[CEU][hapmap];0.90[YRI][hapmap]
rs2016837	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];0.82[EUR][1000 genomes]
rs2412822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];0.89[MKK][hapmap];0.82[TSI][hapmap];0.86[YRI][hapmap]
rs28548859	0.85[ASN][1000 genomes]
rs2918945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.97[LWK][hapmap];0.89[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs2918946	0.81[EUR][1000 genomes]
rs3087657	0.85[ASW][hapmap]
rs4544217	0.83[ASN][1000 genomes]
rs530074	1.00[CEU][hapmap];0.81[EUR][1000 genomes]
rs563940	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];0.81[CHD][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap];0.82[EUR][1000 genomes];0.80[ASN][1000 genomes]
rs597705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[LWK][hapmap];1.00[MEX][hapmap];1.00[MKK][hapmap];0.82[TSI][hapmap];1.00[YRI][hapmap];0.81[EUR][1000 genomes]
rs638224	1.00[CEU][hapmap];0.95[YRI][hapmap];0.81[EUR][1000 genomes]
rs663214	0.85[ASW][hapmap]
rs747714	1.00[CEU][hapmap];0.88[CHB][hapmap];0.82[YRI][hapmap]
rs8042714	1.00[CEU][hapmap];0.88[CHB][hapmap]
rs920339	1.00[CEU][hapmap];0.91[YRI][hapmap]

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	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	nsv1050263	chr15:44093927-44204047	Strong transcription Flanking Active TSS Weak transcription Bivalent/Poised TSS Enhancers Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	22 gene(s)	inside rSNPs	n/a
6	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
rs678513	TGM5	cis	lymphoblastoid	seeQTL
rs678513	ADAL	cis	Artery Tibial	GTEx
rs678513	ADAL	cis	Adipose Subcutaneous	GTEx
rs678513	ADAL	cis	Nerve Tibial	GTEx
rs678513	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs678513	ADAL	cis	Thyroid	GTEx
rs678513	ADAL	cis	lung	GTEx
rs678513	ADAL	cis	Esophagus Muscularis	GTEx

Chromatin state (count:58 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
2	chr15:44166800-44193800	Weak transcription	Spleen	Spleen
3	chr15:44166800-44196200	Weak transcription	Osteobl	bone
4	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
5	chr15:44173800-44193600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
6	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
7	chr15:44174200-44194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
8	chr15:44174200-44195800	Weak transcription	HUES48 Cell Line	embryonic stem cell
9	chr15:44174200-44195800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
10	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
11	chr15:44176800-44193600	Weak transcription	HUES6 Cell Line	embryonic stem cell
12	chr15:44178200-44197800	Weak transcription	NHLF	lung
13	chr15:44179400-44193600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr15:44180000-44195800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
15	chr15:44183200-44193000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
16	chr15:44183400-44197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:44184000-44194200	Weak transcription	HUVEC	blood vessel
18	chr15:44186200-44193200	Weak transcription	HMEC	breast
19	chr15:44186200-44197800	Weak transcription	NHEK	skin
20	chr15:44187000-44203600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
21	chr15:44187600-44196000	Weak transcription	Fetal Muscle Leg	muscle
22	chr15:44187800-44195800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
23	chr15:44188400-44194600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
24	chr15:44189200-44193400	Weak transcription	Brain Anterior Caudate	brain
25	chr15:44189200-44197800	Weak transcription	NH-A	brain
26	chr15:44189400-44193600	Weak transcription	NHDF-Ad	bronchial
27	chr15:44190000-44194800	Strong transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:44190600-44193600	Enhancers	Fetal Heart	heart
29	chr15:44190800-44194400	Enhancers	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:44191000-44195200	Strong transcription	Brain Dorsolateral Prefrontal Cortex	brain
31	chr15:44191000-44197600	Weak transcription	Brain Germinal Matrix	brain
32	chr15:44191200-44207400	Weak transcription	Ovary	ovary
33	chr15:44191400-44193600	Weak transcription	Fetal Stomach	stomach
34	chr15:44191400-44194400	Genic enhancers	Brain Cingulate Gyrus	brain
35	chr15:44191800-44193400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
36	chr15:44191800-44194600	Genic enhancers	Brain Inferior Temporal Lobe	brain
37	chr15:44192000-44194000	Enhancers	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
38	chr15:44192000-44194400	Genic enhancers	Foreskin Melanocyte Primary Cells skin03	Skin
39	chr15:44192200-44193000	Enhancers	HepG2	liver
40	chr15:44192200-44193600	Weak transcription	Brain Angular Gyrus	brain
41	chr15:44192200-44193600	Weak transcription	Fetal Brain Female	brain
42	chr15:44192200-44194200	Enhancers	Foreskin Fibroblast Primary Cells skin01	Skin
43	chr15:44192200-44196200	Weak transcription	Right Ventricle	heart
44	chr15:44192200-44203600	Weak transcription	Left Ventricle	heart
45	chr15:44192400-44193000	Strong transcription	Cortex derived primary cultured neurospheres	brain
46	chr15:44192400-44194000	Enhancers	Primary hematopoietic stem cells G-CSF-mobilized Male	--
47	chr15:44192400-44194400	Genic enhancers	Foreskin Melanocyte Primary Cells skin01	Skin
48	chr15:44192400-44194600	Genic enhancers	Brain Substantia Nigra	brain
49	chr15:44192400-44203200	Weak transcription	Right Atrium	heart
50	chr15:44192600-44193600	Weak transcription	Primary hematopoietic stem cells short term culture	blood

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