Variant report

Variant	rs7181039
Chromosome Location	chr15:44179112-44179113
allele	A/G
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	POLR2A	chr15:44179013-44179948	U87	brain:	n/a	n/a
2	POLR2A	chr15:44178797-44179524	Hela-S3	cervix:	n/a	n/a
3	POLR2A	chr15:44178678-44184598	Hela-S3	cervix:	n/a	n/a
4	POLR2A	chr15:44178474-44179663	PANC-1	pancreas:	n/a	n/a
5	POLR2A	chr15:44178632-44179398	GM12892	blood:	n/a	n/a
6	POLR2A	chr15:44178744-44179641	GM12892	blood:	n/a	n/a
7	POLR2A	chr15:44179007-44180033	U87	brain:	n/a	n/a
8	POLR2A	chr15:44177710-44184889	K562	blood:	n/a	n/a
9	POLR2A	chr15:44178807-44179157	HL-60	blood:	n/a	n/a
10	POLR2A	chr15:44178575-44179204	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr15:44177766..44179908-chr15:44181955..44184452,3	K562	blood:

Variant related genes	Relation type
FRMD5	TF binding region

Extended variants
information (count: 87 )
Associated
traits (count: 9 )

rSNPs within LD-proxies of this variant (count:81)

rs_ID	r²[population]
rs10163054	0.88[CEU][hapmap]
rs10438303	1.00[CEU][hapmap]
rs11070408	0.88[CEU][hapmap]
rs11852767	0.92[AMR][1000 genomes];0.98[EUR][1000 genomes]
rs11856495	0.96[EUR][1000 genomes]
rs11856795	1.00[CEU][hapmap];0.96[YRI][hapmap];0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs12440573	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs12441127	1.00[CEU][hapmap]
rs12441861	1.00[CEU][hapmap]
rs12441984	1.00[CEU][hapmap];0.93[YRI][hapmap];0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs12442297	1.00[CEU][hapmap];1.00[CHB][hapmap];0.88[JPT][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.97[AMR][1000 genomes];1.00[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs12702	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs13329084	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs16950562	1.00[CEU][hapmap]
rs16965120	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs16977724	1.00[CEU][hapmap];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs16977798	1.00[CEU][hapmap];0.96[YRI][hapmap];0.88[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs1965794	0.92[EUR][1000 genomes]
rs1965795	0.89[EUR][1000 genomes]
rs2228368	0.90[EUR][1000 genomes]
rs2277531	1.00[CEU][hapmap]
rs2467402	1.00[CEU][hapmap]
rs2467426	0.88[CEU][hapmap]
rs2788	1.00[CEU][hapmap]
rs28413704	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28413881	0.96[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs28437196	0.89[EUR][1000 genomes]
rs28476182	0.95[EUR][1000 genomes]
rs28509275	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs28513374	0.92[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.95[EUR][1000 genomes]
rs28519630	0.96[EUR][1000 genomes]
rs28524541	0.96[EUR][1000 genomes]
rs28531819	0.96[EUR][1000 genomes]
rs28564774	0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28583806	0.90[EUR][1000 genomes]
rs28590651	0.90[EUR][1000 genomes]
rs28636829	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs28674750	0.90[EUR][1000 genomes]
rs28679673	0.96[EUR][1000 genomes]
rs28684672	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs28687459	0.82[AFR][1000 genomes];0.96[EUR][1000 genomes]
rs28696802	0.96[EUR][1000 genomes]
rs28699233	0.87[CEU][hapmap];0.95[EUR][1000 genomes]
rs28707214	0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs28780699	0.96[EUR][1000 genomes]
rs28781888	0.90[EUR][1000 genomes]
rs28823973	1.00[EUR][1000 genomes]
rs28858500	1.00[EUR][1000 genomes]
rs28866846	0.96[EUR][1000 genomes]
rs2955969	0.81[CHB][hapmap]
rs3736180	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3742982	1.00[CEU][hapmap];1.00[YRI][hapmap];0.98[AFR][1000 genomes];0.97[AMR][1000 genomes];0.93[EUR][1000 genomes]
rs3759790	1.00[CEU][hapmap];0.96[EUR][1000 genomes]
rs3759791	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3784275	0.87[CEU][hapmap];0.88[EUR][1000 genomes]
rs3816792	1.00[CEU][hapmap];0.90[EUR][1000 genomes]
rs3825783	1.00[CEU][hapmap];0.89[EUR][1000 genomes]
rs3862142	1.00[CEU][hapmap]
rs4597285	0.89[EUR][1000 genomes]
rs472385	0.91[ASN][1000 genomes]
rs4997480	1.00[CEU][hapmap]
rs56008017	0.90[EUR][1000 genomes]
rs56909447	0.93[EUR][1000 genomes]
rs61390361	0.90[AFR][1000 genomes];0.83[AMR][1000 genomes];1.00[EUR][1000 genomes]
rs67541383	0.97[AMR][1000 genomes];0.98[EUR][1000 genomes];0.91[ASN][1000 genomes]
rs68079546	0.96[EUR][1000 genomes]
rs7169322	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7169988	1.00[CEU][hapmap]
rs7170751	0.96[EUR][1000 genomes]
rs7171750	1.00[CEU][hapmap]
rs7174208	1.00[CEU][hapmap]
rs7175032	1.00[CEU][hapmap]
rs7179388	0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs7183809	0.96[EUR][1000 genomes]
rs8023458	1.00[CEU][hapmap]
rs8023508	0.84[AMR][1000 genomes]
rs8032649	1.00[CEU][hapmap];0.96[YRI][hapmap];0.86[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[EUR][1000 genomes]
rs8033995	1.00[CEU][hapmap]
rs8040839	0.85[AFR][1000 genomes];0.89[EUR][1000 genomes]
rs9944216	1.00[CEU][hapmap];1.00[EUR][1000 genomes]
rs9989313	1.00[CEU][hapmap];0.96[YRI][hapmap];0.87[AFR][1000 genomes];0.80[AMR][1000 genomes];0.96[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:9)

SNP	Gene	Cis/trans	Tissue	Source
rs7181039	ADAL	cis	Adipose Subcutaneous	GTEx
rs7181039	ADAL	cis	Esophagus Muscularis	GTEx
rs7181039	ADAL	cis	Artery Tibial	GTEx
rs7181039	ADAL	cis	lung	GTEx
rs7181039	ADAL	cis	Thyroid	GTEx
rs7181039	ADAL	cis	Nerve Tibial	GTEx
rs7181039	ELL3	Cis_1M	lymphoblastoid	RTeQTL
rs7181039	ADAL	cis	Skin Sun Exposed Lower leg	GTEx
rs7181039	CKMT1A	cis	Esophagus Mucosa	GTEx

Chromatin state (count:77 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr15:44119600-44181800	Weak transcription	Small Intestine	intestine
2	chr15:44119600-44183200	Weak transcription	ES-WA7 Cell Line	embryonic stem cell
3	chr15:44144800-44181000	Weak transcription	HepG2	liver
4	chr15:44146800-44181600	Weak transcription	Gastric	stomach
5	chr15:44151600-44181600	Weak transcription	Sigmoid Colon	Sigmoid Colon
6	chr15:44152600-44180800	Weak transcription	Duodenum Mucosa	Duodenum
7	chr15:44156800-44206400	Weak transcription	Fetal Brain Male	brain
8	chr15:44158600-44180800	Weak transcription	Fetal Lung	lung
9	chr15:44162200-44186000	Weak transcription	HSMM	muscle
10	chr15:44163000-44179400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
11	chr15:44166000-44184600	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
12	chr15:44166400-44186600	Weak transcription	Primary hematopoietic stem cells	blood
13	chr15:44166600-44182600	Weak transcription	HUVEC	blood vessel
14	chr15:44166600-44183800	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
15	chr15:44166800-44193800	Weak transcription	Spleen	Spleen
16	chr15:44166800-44196200	Weak transcription	Osteobl	bone
17	chr15:44168000-44180200	Weak transcription	hESC Derived CD56+ Mesoderm Cultured Cells	ES cell derived
18	chr15:44169000-44181000	Strong transcription	Foreskin Melanocyte Primary Cells skin03	Skin
19	chr15:44170600-44188800	Weak transcription	NHDF-Ad	bronchial
20	chr15:44170800-44180000	Strong transcription	H1 Derived Mesenchymal Stem Cells	ES cell derived
21	chr15:44171600-44181400	Strong transcription	Brain Germinal Matrix	brain
22	chr15:44173000-44182800	Weak transcription	Fetal Muscle Trunk	muscle
23	chr15:44173400-44182400	Weak transcription	Fetal Muscle Leg	muscle
24	chr15:44173400-44183000	Weak transcription	H1 BMP4 Derived Trophoblast Cultured Cells	ES cell derived
25	chr15:44173400-44185800	Strong transcription	Fetal Adrenal Gland	Adrenal Gland
26	chr15:44173600-44184800	Weak transcription	hESC Derived CD56+ Ectoderm Cultured Cells	ES cell derived
27	chr15:44173600-44208000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
28	chr15:44173800-44182800	Weak transcription	HUES64 Cell Line	embryonic stem cell
29	chr15:44173800-44182800	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
30	chr15:44173800-44183000	Weak transcription	H1 Derived Neuronal Progenitor Cultured Cells	ES cell derived
31	chr15:44173800-44186200	Weak transcription	GM12878-XiMat	blood
32	chr15:44173800-44190000	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
33	chr15:44173800-44193600	Weak transcription	iPS-15b Cell Line	embryonic stem cell
34	chr15:44173800-44211600	Weak transcription	H9 Cell Line	embryonic stem cell
35	chr15:44174000-44180800	Weak transcription	Fetal Intestine Large	intestine
36	chr15:44174000-44184400	Strong transcription	Brain Cingulate Gyrus	brain
37	chr15:44174200-44194200	Weak transcription	iPS-20b Cell Line	embryonic stem cell
38	chr15:44174200-44195800	Weak transcription	HUES48 Cell Line	embryonic stem cell
39	chr15:44174200-44195800	Weak transcription	iPS-18 Cell Line	embryonic stem cell
40	chr15:44174200-44211600	Weak transcription	H1 Cell Line	embryonic stem cell
41	chr15:44174600-44180400	Weak transcription	Primary neutrophils fromperipheralblood	blood
42	chr15:44175200-44179400	Strong transcription	H9 Derived Neuron Cultured Cells	ES cell derived
43	chr15:44175400-44180000	Strong transcription	Brain Hippocampus Middle	brain
44	chr15:44175600-44180800	Strong transcription	Fetal Stomach	stomach
45	chr15:44175600-44184400	Strong transcription	Foreskin Melanocyte Primary Cells skin01	Skin
46	chr15:44175800-44179200	Strong transcription	Brain Anterior Caudate	brain
47	chr15:44175800-44179600	Strong transcription	NHEK	skin
48	chr15:44176600-44179200	Weak transcription	Ganglion Eminence derived primary cultured neurospheres	brain
49	chr15:44176600-44182400	Weak transcription	Fetal Thymus	thymus
50	chr15:44176600-44192000	Weak transcription	Hela-S3	cervix

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