Variant report

Variant	rs9806129
Chromosome Location	chr15:44209062-44209063
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44208448..44210061-chr15:44210295..44213108,2	K562	blood:
2	chr15:44196908..44202469-chr15:44206840..44210782,4	K562	blood:

Variant related genes	Relation type
ENSG00000171877	Chromatin interaction

Extended variants
information (count: 33 )
Associated
traits (count: 1 )

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

rs_ID	r²[population]
rs1008183	0.91[EUR][1000 genomes]
rs11070413	0.88[AFR][1000 genomes];0.92[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11070415	0.81[AFR][1000 genomes];1.00[EUR][1000 genomes]
rs11070416	0.83[AFR][1000 genomes];0.89[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs11630936	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs11631901	0.94[EUR][1000 genomes]
rs11635039	0.94[EUR][1000 genomes]
rs11637468	0.85[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs12439442	0.87[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs12440402	0.94[EUR][1000 genomes]
rs12442168	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes]
rs16944774	0.84[AMR][1000 genomes];0.94[EUR][1000 genomes];0.95[ASN][1000 genomes]
rs16945686	0.88[AFR][1000 genomes];0.97[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs16950215	0.82[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs2306674	0.94[EUR][1000 genomes]
rs28377221	0.89[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.94[ASN][1000 genomes]
rs28438984	0.90[AMR][1000 genomes];1.00[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs28542819	0.86[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs28599486	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.96[ASN][1000 genomes]
rs28685813	0.92[EUR][1000 genomes]
rs28706414	0.86[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs3742981	0.91[AFR][1000 genomes];0.92[AMR][1000 genomes];0.97[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs3850777	0.97[EUR][1000 genomes]
rs530074	0.91[ASN][1000 genomes]
rs55927923	0.97[EUR][1000 genomes]
rs60484809	0.88[AMR][1000 genomes];0.94[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs7178452	0.81[AFR][1000 genomes];0.97[EUR][1000 genomes]
rs9920164	0.92[AMR][1000 genomes];0.94[EUR][1000 genomes];0.97[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:1)

SNP	Gene	Cis/trans	Tissue	Source
rs9806129	ELL3	Cis_1M	lymphoblastoid	RTeQTL

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

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
2	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
3	chr15:44196400-44212200	Weak transcription	Fetal Stomach	stomach
4	chr15:44196400-44216800	Weak transcription	H9 Derived Neuron Cultured Cells	ES cell derived
5	chr15:44198000-44211600	Weak transcription	iPS-18 Cell Line	embryonic stem cell
6	chr15:44198200-44217600	Weak transcription	Brain Germinal Matrix	brain
7	chr15:44206000-44213400	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
8	chr15:44206200-44210800	Weak transcription	HSMMtube	muscle
9	chr15:44206200-44211400	Weak transcription	Brain Dorsolateral Prefrontal Cortex	brain
10	chr15:44206200-44211600	Weak transcription	Aorta	Aorta
11	chr15:44206600-44211000	Weak transcription	Cortex derived primary cultured neurospheres	brain
12	chr15:44206600-44211800	Weak transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
13	chr15:44206600-44212000	Weak transcription	Muscle Satellite Cultured Cells	--
14	chr15:44206800-44210000	Weak transcription	NH-A	brain
15	chr15:44206800-44212000	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
16	chr15:44206800-44212000	Weak transcription	NHDF-Ad	bronchial
17	chr15:44206800-44217800	Weak transcription	Foreskin Fibroblast Primary Cells skin02	Skin
18	chr15:44207000-44210000	Weak transcription	HMEC	breast
19	chr15:44207000-44212200	Weak transcription	Osteobl	bone
20	chr15:44207000-44214200	Weak transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
21	chr15:44207200-44214600	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
22	chr15:44208000-44217800	Weak transcription	NHLF	lung
23	chr15:44208200-44211800	Weak transcription	Fetal Lung	lung
24	chr15:44208400-44211400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
25	chr15:44208400-44211600	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
26	chr15:44208400-44212200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung
27	chr15:44208400-44212400	Weak transcription	Stomach Smooth Muscle	stomach
28	chr15:44208400-44212800	Weak transcription	Right Atrium	heart
29	chr15:44208400-44213000	Weak transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
30	chr15:44208400-44213000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
31	chr15:44208400-44213000	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
32	chr15:44208400-44213200	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
33	chr15:44208600-44209800	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
34	chr15:44208600-44210400	Weak transcription	Fetal Brain Male	brain
35	chr15:44208600-44210600	Weak transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
36	chr15:44208600-44210800	Weak transcription	Brain Inferior Temporal Lobe	brain
37	chr15:44208600-44210800	Weak transcription	Brain Substantia Nigra	brain
38	chr15:44208600-44211000	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
39	chr15:44208600-44211000	Weak transcription	Brain Hippocampus Middle	brain
40	chr15:44208600-44211000	Weak transcription	Fetal Muscle Leg	muscle
41	chr15:44208600-44211600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
42	chr15:44208600-44211600	Weak transcription	HUES48 Cell Line	embryonic stem cell
43	chr15:44208600-44211600	Weak transcription	HUES64 Cell Line	embryonic stem cell
44	chr15:44208600-44211600	Weak transcription	iPS-20b Cell Line	embryonic stem cell
45	chr15:44208600-44211800	Weak transcription	HUES6 Cell Line	embryonic stem cell
46	chr15:44208600-44212000	Weak transcription	Rectal Smooth Muscle	rectum
47	chr15:44208600-44213000	Weak transcription	Right Ventricle	heart
48	chr15:44208800-44210000	Weak transcription	Brain Anterior Caudate	brain
49	chr15:44208800-44210800	Weak transcription	Brain Angular Gyrus	brain
50	chr15:44208800-44210800	Weak transcription	Brain Cingulate Gyrus	brain

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