Variant report

Variant	rs12440402
Chromosome Location	chr15:44202014-44202015
allele	C/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

Extended variants
information (count: 34 )
Associated
traits (count: 2 )

rSNPs within LD-proxies of this variant (count:28)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.86[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs1077421	0.92[CHB][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs11070413	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.94[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11070415	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11070416	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs11630936	1.00[CEU][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs11631901	1.00[CEU][hapmap];0.92[CHB][hapmap];0.87[JPT][hapmap];0.87[AMR][1000 genomes];0.89[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.85[AMR][1000 genomes];0.89[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12439442	0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12442168	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.82[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs16944774	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs16945686	1.00[CEU][hapmap];0.83[AFR][1000 genomes];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs16950215	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.88[ASN][1000 genomes]
rs2306674	1.00[CEU][hapmap];0.93[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28377221	0.91[EUR][1000 genomes]
rs28438984	0.94[EUR][1000 genomes]
rs28542819	0.91[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs28599486	0.94[EUR][1000 genomes]
rs28685813	0.92[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs28706414	0.91[EUR][1000 genomes]
rs3742981	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs3850777	1.00[CEU][hapmap];0.92[CHB][hapmap];0.93[JPT][hapmap];0.95[AMR][1000 genomes];0.97[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs55927923	0.93[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs60484809	0.82[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs7178452	1.00[CEU][hapmap];0.92[CHB][hapmap];1.00[JPT][hapmap];0.91[AMR][1000 genomes];0.91[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs9806129	0.94[EUR][1000 genomes]
rs9920164	1.00[CEU][hapmap];0.94[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:2)

SNP	Gene	Cis/trans	Tissue	Source
rs12440402	ADAL	cis	Nerve Tibial	GTEx
rs12440402	ELL3	Cis_1M	lymphoblastoid	RTeQTL

Chromatin state (count:56 , 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	chr15:44194400-44204000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
10	chr15:44194600-44203000	Weak transcription	HMEC	breast
11	chr15:44194600-44203200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
12	chr15:44194600-44208200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
13	chr15:44196400-44203600	Weak transcription	Fetal Muscle Trunk	muscle
14	chr15:44196400-44203800	Weak transcription	Fetal Heart	heart
15	chr15:44196400-44204600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
16	chr15:44196400-44205200	Weak transcription	HUES64 Cell Line	embryonic stem cell
17	chr15:44196400-44207600	Weak transcription	Gastric	stomach
18	chr15:44196400-44208000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
19	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
20	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
21	chr15:44196600-44204600	Weak transcription	Hela-S3	cervix
22	chr15:44196600-44205400	Weak transcription	ES-I3 Cell Line	embryonic stem cell
23	chr15:44196600-44208200	Weak transcription	HUES48 Cell Line	embryonic stem cell
24	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
25	chr15:44196800-44202400	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
26	chr15:44196800-44203000	Weak transcription	Osteobl	bone
27	chr15:44196800-44203600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
28	chr15:44198000-44205200	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
29	chr15:44198000-44211600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
30	chr15:44198200-44203400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
31	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
32	chr15:44198400-44202400	Weak transcription	Brain Angular Gyrus	brain
33	chr15:44198400-44203000	Weak transcription	Brain Anterior Caudate	brain
34	chr15:44198400-44208000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
35	chr15:44198600-44202400	Weak transcription	NHLF	lung
36	chr15:44198600-44203000	Weak transcription	Cortex derived primary cultured neurospheres	brain
37	chr15:44198600-44203000	Weak transcription	Brain Substantia Nigra	brain
38	chr15:44198600-44203200	Weak transcription	NHEK	skin
39	chr15:44198600-44203400	Weak transcription	Brain Cingulate Gyrus	brain
40	chr15:44198600-44205400	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr15:44198800-44203200	Weak transcription	Brain Hippocampus Middle	brain
42	chr15:44198800-44203400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:44198800-44207600	Weak transcription	Fetal Brain Female	brain
44	chr15:44200000-44202200	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
45	chr15:44200000-44208000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
46	chr15:44200600-44202600	Strong transcription	NH-A	brain
47	chr15:44200800-44202200	Strong transcription	Brain Inferior Temporal Lobe	brain
48	chr15:44200800-44203000	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
49	chr15:44201200-44208000	Weak transcription	Fetal Muscle Leg	muscle
50	chr15:44201400-44202400	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived

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