Variant report

Variant	rs3742981
Chromosome Location	chr15:44216577-44216578
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44209238..44212710-chr15:44213931..44216790,3	K562	blood:
2	chr15:44209238..44211799-chr15:44214318..44216790,2	K562	blood:

Variant related genes	Relation type
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 40 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:35)

rs_ID	r²[population]
rs1008183	1.00[CEU][hapmap];0.95[GIH][hapmap];0.82[MEX][hapmap];0.84[MKK][hapmap];0.89[TSI][hapmap];0.88[EUR][1000 genomes]
rs10152658	0.82[EUR][1000 genomes]
rs11070413	1.00[ASW][hapmap];1.00[CEU][hapmap];0.82[GIH][hapmap];0.90[LWK][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];1.00[YRI][hapmap];0.97[AFR][1000 genomes];1.00[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11070414	0.84[MEX][hapmap]
rs11070415	1.00[CEU][hapmap];0.86[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11070416	0.88[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs11630936	1.00[CEU][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11631901	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs11635039	1.00[CEU][hapmap];0.97[EUR][1000 genomes]
rs11637468	1.00[CEU][hapmap];1.00[CHB][hapmap];0.94[JPT][hapmap];0.95[YRI][hapmap];0.94[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs12439442	0.82[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440402	1.00[CEU][hapmap];0.91[EUR][1000 genomes]
rs12442168	1.00[CEU][hapmap];0.95[GIH][hapmap];1.00[MEX][hapmap];1.00[TSI][hapmap];0.92[AMR][1000 genomes];0.91[EUR][1000 genomes]
rs16944774	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]
rs16945686	0.86[ASW][hapmap];1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];1.00[JPT][hapmap];0.81[LWK][hapmap];0.94[MEX][hapmap];1.00[TSI][hapmap];0.89[YRI][hapmap];0.89[AFR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs16950215	0.92[ASW][hapmap];1.00[CEU][hapmap];0.90[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.87[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs17505315	0.88[TSI][hapmap]
rs2306674	1.00[CEU][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.91[EUR][1000 genomes]
rs28377221	0.96[AFR][1000 genomes];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs28438984	0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs28525216	1.00[TSI][hapmap]
rs28542819	0.85[AFR][1000 genomes];0.90[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs28599486	0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs28670868	0.83[EUR][1000 genomes]
rs28685813	0.89[EUR][1000 genomes]
rs28706414	0.95[AFR][1000 genomes];0.98[AMR][1000 genomes];1.00[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs2918945	0.84[MEX][hapmap]
rs3850777	1.00[CEU][hapmap];0.87[MEX][hapmap];1.00[TSI][hapmap];0.94[EUR][1000 genomes]
rs530074	0.88[CHB][hapmap];0.94[JPT][hapmap];0.93[ASN][1000 genomes]
rs55927923	0.94[EUR][1000 genomes];0.82[ASN][1000 genomes]
rs60484809	0.92[AMR][1000 genomes];0.91[EUR][1000 genomes];0.93[ASN][1000 genomes]
rs7178452	0.92[ASW][hapmap];1.00[CEU][hapmap];0.85[LWK][hapmap];0.82[MEX][hapmap];1.00[TSI][hapmap];0.86[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs8031749	0.83[EUR][1000 genomes]
rs9806129	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs9920164	1.00[CEU][hapmap];1.00[CHB][hapmap];0.93[CHD][hapmap];0.82[GIH][hapmap];1.00[JPT][hapmap];0.88[MEX][hapmap];1.00[TSI][hapmap];0.96[AMR][1000 genomes];0.97[EUR][1000 genomes];0.99[ASN][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:3)

SNP	Gene	Cis/trans	Tissue	Source
rs3742981	ELL3	cis	lymphoblastoid	seeQTL
rs3742981	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs3742981	ADAL	cis	Nerve Tibial	GTEx

Chromatin state (count:49 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
2	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
3	chr15:44206800-44217800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
4	chr15:44208000-44217800	Weak transcription	NHLF	lung
5	chr15:44208800-44222600	Weak transcription	Fetal Brain Female	brain
6	chr15:44211800-44221800	Weak transcription	Cortex derived primary cultured neurospheres	brain
7	chr15:44211800-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
8	chr15:44212400-44218000	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
9	chr15:44212400-44220600	Weak transcription	Sigmoid Colon	Sigmoid Colon
10	chr15:44212400-44225000	Weak transcription	Foreskin Melanocyte Primary Cells skin03	Skin
11	chr15:44212600-44218000	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
12	chr15:44213000-44217600	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
13	chr15:44213400-44217600	Weak transcription	Breast Myoepithelial Primary Cells	Breast
14	chr15:44213400-44217800	Weak transcription	ES-I3 Cell Line	embryonic stem cell
15	chr15:44213400-44217800	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr15:44213400-44218400	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
17	chr15:44213400-44221600	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
18	chr15:44213600-44217800	Weak transcription	HUES64 Cell Line	embryonic stem cell
19	chr15:44213600-44218000	Weak transcription	iPS-15b Cell Line	embryonic stem cell
20	chr15:44213600-44219800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
21	chr15:44213800-44217600	Weak transcription	HUES6 Cell Line	embryonic stem cell
22	chr15:44213800-44217800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
23	chr15:44214000-44217000	Weak transcription	NHDF-Ad	bronchial
24	chr15:44214000-44217600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
25	chr15:44214000-44221600	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
26	chr15:44214000-44224400	Weak transcription	Right Atrium	heart
27	chr15:44214200-44217800	Weak transcription	HUES48 Cell Line	embryonic stem cell
28	chr15:44214200-44217800	Weak transcription	Fetal Muscle Leg	muscle
29	chr15:44214200-44218000	Weak transcription	H1 Cell Line	embryonic stem cell
30	chr15:44214200-44218200	Weak transcription	H9 Cell Line	embryonic stem cell
31	chr15:44214400-44218000	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
32	chr15:44214400-44224000	Weak transcription	HSMMtube	muscle
33	chr15:44214600-44217000	Strong transcription	Brain Hippocampus Middle	brain
34	chr15:44214600-44217600	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
35	chr15:44214800-44216600	Weak transcription	Foreskin Fibroblast Primary Cells skin01	Skin
36	chr15:44214800-44217800	Weak transcription	HMEC	breast
37	chr15:44215000-44218000	Weak transcription	NHEK	skin
38	chr15:44215200-44218000	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
39	chr15:44215400-44216800	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
40	chr15:44215600-44216600	Strong transcription	NH-A	brain
41	chr15:44215600-44216800	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
42	chr15:44215800-44221400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
43	chr15:44216000-44216800	Enhancers	Fetal Heart	heart
44	chr15:44216200-44218000	Weak transcription	Brain Cingulate Gyrus	brain
45	chr15:44216400-44217800	Weak transcription	Brain Angular Gyrus	brain
46	chr15:44216400-44217800	Weak transcription	Brain Inferior Temporal Lobe	brain
47	chr15:44216400-44217800	Weak transcription	Fetal Adrenal Gland	Adrenal Gland
48	chr15:44216400-44218600	Weak transcription	Brain Substantia Nigra	brain
49	chr15:44216400-44220600	Weak transcription	Brain Anterior Caudate	brain

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