Variant report

Variant	rs563940
Chromosome Location	chr15:44199309-44199310
allele	G/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44196106..44199754-chr15:44205350..44208904,3	K562	blood:

Extended variants
information (count: 27 )
Associated
traits (count: 7 )

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

rs_ID	r²[population]
rs1077421	1.00[CEU][hapmap];0.95[TSI][hapmap];0.95[EUR][1000 genomes]
rs11070414	0.86[ASW][hapmap];1.00[CEU][hapmap];0.85[MEX][hapmap];0.85[MKK][hapmap];1.00[TSI][hapmap];0.95[EUR][1000 genomes]
rs11635039	0.87[CHB][hapmap];0.94[JPT][hapmap];0.89[ASN][1000 genomes]
rs1545182	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[EUR][1000 genomes]
rs2016837	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]
rs2412822	1.00[ASW][hapmap];1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[CHD][hapmap];1.00[JPT][hapmap];0.94[MEX][hapmap];0.86[MKK][hapmap];0.95[TSI][hapmap];0.81[AMR][1000 genomes];0.92[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28548859	0.94[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs2918945	1.00[ASW][hapmap];1.00[CEU][hapmap];0.92[GIH][hapmap];0.85[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.87[YRI][hapmap];0.84[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs2918946	0.85[AFR][1000 genomes];0.95[EUR][1000 genomes]
rs3087657	0.85[ASW][hapmap]
rs4544217	0.94[EUR][1000 genomes];0.87[ASN][1000 genomes]
rs472797	0.92[EUR][1000 genomes]
rs530074	1.00[CEU][hapmap];0.84[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs589649	0.92[EUR][1000 genomes]
rs597705	1.00[ASW][hapmap];1.00[CEU][hapmap];0.94[MEX][hapmap];0.97[MKK][hapmap];0.95[TSI][hapmap];0.91[YRI][hapmap];0.88[AFR][1000 genomes];0.89[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs638224	1.00[CEU][hapmap];0.87[YRI][hapmap];0.86[AFR][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];0.94[MEX][hapmap];0.97[MKK][hapmap];0.86[TSI][hapmap];0.91[YRI][hapmap]
rs747714	1.00[CEU][hapmap];0.88[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs8042714	1.00[CEU][hapmap];0.88[CHB][hapmap];0.94[JPT][hapmap];0.94[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs920339	1.00[CEU][hapmap];0.82[YRI][hapmap];0.81[AFR][1000 genomes];0.92[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	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:7)

SNP	Gene	Cis/trans	Tissue	Source
rs563940	ADAL	cis	Thyroid	GTEx
rs563940	CKMT1A	cis	Esophagus Mucosa	GTEx
rs563940	ADAL	cis	Esophagus Muscularis	GTEx
rs563940	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs563940	ADAL	cis	Nerve Tibial	GTEx
rs563940	TGM5	cis	lymphoblastoid	seeQTL
rs563940	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:54 , 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	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
3	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
4	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
5	chr15:44187000-44203600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
6	chr15:44191200-44207400	Weak transcription	Ovary	ovary
7	chr15:44192200-44203600	Weak transcription	Left Ventricle	heart
8	chr15:44192400-44203200	Weak transcription	Right Atrium	heart
9	chr15:44194400-44202000	Weak transcription	NHDF-Ad	bronchial
10	chr15:44194400-44204000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
11	chr15:44194600-44203000	Weak transcription	HMEC	breast
12	chr15:44194600-44203200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
13	chr15:44194600-44208200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
14	chr15:44194800-44200800	Weak transcription	HUVEC	blood vessel
15	chr15:44195000-44200000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
16	chr15:44196400-44203600	Weak transcription	Fetal Muscle Trunk	muscle
17	chr15:44196400-44203800	Weak transcription	Fetal Heart	heart
18	chr15:44196400-44204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
19	chr15:44196400-44205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
20	chr15:44196400-44207600	Weak transcription	Gastric	stomach
21	chr15:44196400-44208000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
22	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
23	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
24	chr15:44196600-44204600	Weak transcription	Hela-S3	cervix
25	chr15:44196600-44205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
26	chr15:44196600-44208200	Weak transcription	HUES48 Cell Line	embryonic stem cell
27	chr15:44196800-44201800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
28	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
29	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
30	chr15:44196800-44203000	Weak transcription	Osteobl	bone
31	chr15:44196800-44203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
32	chr15:44197000-44200400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:44198000-44199600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
34	chr15:44198000-44205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
35	chr15:44198000-44211600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
36	chr15:44198200-44203400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
37	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
38	chr15:44198400-44202400	Weak transcription	Brain Angular Gyrus	brain
39	chr15:44198400-44203000	Weak transcription	Brain Anterior Caudate	brain
40	chr15:44198400-44208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
41	chr15:44198600-44200600	Weak transcription	NH-A	brain
42	chr15:44198600-44200800	Weak transcription	Brain Inferior Temporal Lobe	brain
43	chr15:44198600-44202400	Weak transcription	NHLF	lung
44	chr15:44198600-44203000	Weak transcription	Cortex derived primary cultured neurospheres	brain
45	chr15:44198600-44203000	Weak transcription	Brain Substantia Nigra	brain
46	chr15:44198600-44203200	Weak transcription	NHEK	skin
47	chr15:44198600-44203400	Weak transcription	Brain Cingulate Gyrus	brain
48	chr15:44198600-44205400	Weak transcription	HUES6 Cell Line	embryonic stem cell
49	chr15:44198800-44201600	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
50	chr15:44198800-44203200	Weak transcription	Brain Hippocampus Middle	brain

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