Variant report

Variant	rs16944774
Chromosome Location	chr15:44195789-44195790
allele	A/C
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr15:44195722..44196644-chr15:44511206..44512558,6	MCF-7	breast:
2	chr15:44185248..44189822-chr15:44193811..44195914,4	K562	blood:
3	chr15:44195719..44197034-chr15:44358046..44359172,5	MCF-7	breast:
4	chr15:44190087..44193923-chr15:44195170..44198299,3	K562	blood:
5	chr15:44194479..44197065-chr15:44202126..44203842,2	K562	blood:
6	chr15:44195679..44196674-chr15:44357585..44358692,5	K562	blood:
7	chr15:44195565..44197593-chr15:44201459..44203626,2	K562	blood:

Variant related genes	Relation type
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 35 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:29)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];0.86[EUR][1000 genomes]
rs11070413	1.00[CEU][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11070415	1.00[CEU][hapmap];0.94[EUR][1000 genomes]
rs11070416	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs11630936	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11631901	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.87[CHB][hapmap];0.93[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12439442	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs12440402	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs12442168	1.00[CEU][hapmap];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs16945686	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.97[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16950215	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs2306674	1.00[CEU][hapmap];0.80[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28377221	0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28438984	0.90[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28542819	0.82[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs28599486	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28685813	0.92[EUR][1000 genomes]
rs28706414	0.90[AMR][1000 genomes];0.91[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs3742981	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs524908	0.80[JPT][hapmap]
rs530074	0.94[JPT][hapmap];0.92[ASN][1000 genomes]
rs55927923	0.97[EUR][1000 genomes];0.85[ASN][1000 genomes]
rs60484809	0.92[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs7178452	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs9806129	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs9920164	1.00[CEU][hapmap];0.87[CHB][hapmap];1.00[JPT][hapmap];0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs16944774	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs16944774	ADAL	cis	Nerve Tibial	GTEx
rs16944774	ADAL	cis	Artery Tibial	GTEx

Chromatin state (count:60 , 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	chr15:44166800-44196200	Weak transcription	Osteobl	bone
3	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
4	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
5	chr15:44174200-44195800	Weak transcription	HUES48 Cell Line	embryonic stem cell
6	chr15:44174200-44195800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
7	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
8	chr15:44178200-44197800	Weak transcription	NHLF	lung
9	chr15:44180000-44195800	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
10	chr15:44183400-44197800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
11	chr15:44186200-44197800	Weak transcription	NHEK	skin
12	chr15:44187000-44203600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
13	chr15:44187600-44196000	Weak transcription	Fetal Muscle Leg	muscle
14	chr15:44187800-44195800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
15	chr15:44189200-44197800	Weak transcription	NH-A	brain
16	chr15:44191000-44197600	Weak transcription	Brain Germinal Matrix	brain
17	chr15:44191200-44207400	Weak transcription	Ovary	ovary
18	chr15:44192200-44196200	Weak transcription	Right Ventricle	heart
19	chr15:44192200-44203600	Weak transcription	Left Ventricle	heart
20	chr15:44192400-44203200	Weak transcription	Right Atrium	heart
21	chr15:44192600-44195800	Weak transcription	Hela-S3	cervix
22	chr15:44192600-44196000	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
23	chr15:44192600-44196200	Genic enhancers	Brain Hippocampus Middle	brain
24	chr15:44192800-44196200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
25	chr15:44193000-44196200	Weak transcription	HepG2	liver
26	chr15:44193400-44195800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
27	chr15:44193800-44195800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
28	chr15:44193800-44195800	Weak transcription	K562	blood
29	chr15:44193800-44196000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:44194000-44195800	Weak transcription	Cortex derived primary cultured neurospheres	brain
31	chr15:44194000-44195800	Weak transcription	Fetal Stomach	stomach
32	chr15:44194000-44196000	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
33	chr15:44194000-44197800	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
34	chr15:44194000-44198000	Weak transcription	hESC Derived CD184+ Endoderm Cultured Cells	ES cell derived
35	chr15:44194200-44196000	Weak transcription	Brain Angular Gyrus	brain
36	chr15:44194200-44196200	Weak transcription	Brain Anterior Caudate	brain
37	chr15:44194200-44196400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
38	chr15:44194400-44195800	Weak transcription	HUES6 Cell Line	embryonic stem cell
39	chr15:44194400-44195800	Weak transcription	HUES64 Cell Line	embryonic stem cell
40	chr15:44194400-44195800	Strong transcription	Brain Cingulate Gyrus	brain
41	chr15:44194400-44196400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
42	chr15:44194400-44202000	Weak transcription	NHDF-Ad	bronchial
43	chr15:44194400-44204000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr15:44194600-44195800	Weak transcription	iPS-15b Cell Line	embryonic stem cell
45	chr15:44194600-44195800	Strong transcription	Brain Inferior Temporal Lobe	brain
46	chr15:44194600-44197800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
47	chr15:44194600-44203000	Weak transcription	HMEC	breast
48	chr15:44194600-44203200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
49	chr15:44194600-44208200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
50	chr15:44194800-44195800	Weak transcription	ES-WA7 Cell Line	embryonic stem cell

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