Variant report

Variant	rs4449041
Chromosome Location	chr18:44334496-44334497
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	BHLHE40	chr18:44334478-44334576	GM12878	blood:	n/a	n/a
2	MEF2A	chr18:44334251-44334532	GM12878	blood:	n/a	n/a
3	RUNX3	chr18:44334181-44334601	GM12878	blood:	n/a	n/a
4	RUNX3	chr18:44334204-44334567	GM12878	blood:	n/a	n/a
5	RCOR1	chr18:44334428-44334525	GM12878	blood:	n/a	n/a
6	EP300	chr18:44334336-44334539	GM12878	blood:	n/a	chr18:44334376-44334390

Variant related genes	Relation type
ENSG00000270112	TF binding region

Extended variants
information (count: 31 )
Associated
traits (count: 3 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs11082558	0.88[ASN][1000 genomes]
rs12454436	0.89[CHB][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16940040	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs16940043	0.94[AFR][1000 genomes];0.94[AMR][1000 genomes];0.97[EUR][1000 genomes];0.92[ASN][1000 genomes]
rs2298778	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs3809962	1.00[ASW][hapmap];1.00[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];1.00[LWK][hapmap];0.90[MEX][hapmap];1.00[MKK][hapmap];0.93[YRI][hapmap];0.99[AFR][1000 genomes];0.89[AMR][1000 genomes];0.93[ASN][1000 genomes]
rs3893181	0.86[CHD][hapmap];0.89[JPT][hapmap];0.88[ASN][1000 genomes]
rs4121690	0.81[ASN][1000 genomes]
rs62097220	0.82[ASN][1000 genomes]
rs7229175	0.95[AFR][1000 genomes]
rs7237805	0.84[JPT][hapmap];0.82[ASN][1000 genomes]
rs73434915	1.00[AFR][1000 genomes];1.00[AMR][1000 genomes];0.99[EUR][1000 genomes];0.97[ASN][1000 genomes]
rs8085861	0.85[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:18 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv428355	chr18:44160181-44406285	Weak transcription Bivalent Enhancer Flanking Active TSS Enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS Strong transcription ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	5 gene(s)	inside rSNPs	diseases
2	nsv9629	chr18:44264693-44757511	Enhancers Weak transcription Active TSS Flanking Active TSS Strong transcription Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	28 gene(s)	inside rSNPs	diseases
3	nsv909591	chr18:44279892-44370518	Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
4	nsv909592	chr18:44279892-44385150	Weak transcription Enhancers Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Active TSS Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
5	nsv909593	chr18:44279892-44396246	Weak transcription Enhancers Bivalent Enhancer Active TSS Flanking Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
6	nsv909594	chr18:44279892-44400621	Weak transcription Enhancers Bivalent/Poised TSS Flanking Active TSS Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
7	nsv909595	chr18:44279892-44422661	Enhancers Weak transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
8	nsv909597	chr18:44291419-44385150	Active TSS Flanking Active TSS Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv909598	chr18:44291419-44422661	Strong transcription Weak transcription Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
10	nsv909599	chr18:44294722-44385150	Weak transcription Flanking Active TSS Bivalent/Poised TSS Enhancers Flanking Bivalent TSS/Enh Active TSS Bivalent Enhancer Strong transcription ZNF genes & repeats Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
11	nsv909600	chr18:44294722-44396246	Active TSS Enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
12	nsv909601	chr18:44294722-44400621	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Active TSS Strong transcription Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
13	nsv909602	chr18:44294722-44422661	Weak transcription Enhancers Flanking Bivalent TSS/Enh Bivalent Enhancer Strong transcription Active TSS Bivalent/Poised TSS Flanking Active TSS ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	4 gene(s)	inside rSNPs	diseases
14	nsv909603	chr18:44300281-44335724	Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent/Poised TSS Weak transcription Active TSS ZNF genes & repeats Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
15	nsv909604	chr18:44300281-44370518	Enhancers Flanking Bivalent TSS/Enh Bivalent/Poised TSS Active TSS Weak transcription Flanking Active TSS Bivalent Enhancer ZNF genes & repeats Transcr. at gene 5' and 3' Strong transcription	TF binding region CpG island Chromatin interactive region lncRNA	3 gene(s)	inside rSNPs	diseases
16	nsv909605	chr18:44316719-44422661	Flanking Bivalent TSS/Enh Weak transcription Strong transcription Enhancers Bivalent Enhancer Bivalent/Poised TSS Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
17	nsv909606	chr18:44318548-44422661	Weak transcription Bivalent Enhancer Enhancers Bivalent/Poised TSS Strong transcription Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh ZNF genes & repeats Transcr. at gene 5' and 3' Genic enhancers	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases
18	nsv909607	chr18:44320836-44422661	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS Flanking Active TSS Active TSS ZNF genes & repeats Genic enhancers Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA target site	3 gene(s)	inside rSNPs	diseases

mRNA abundance (count:3)

SNP	Gene	Cis/trans	Tissue	Source
rs4449041	ST8SIA5	cis	lymphoblastoid	seeQTL
rs4449041	ST8SIA5	cis	multi-tissue	Pritchard
rs4449041	SMAD2	cis	parietal	SCAN

Chromatin state (count:29 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44332600-44335000	Weak transcription	HSMMtube	muscle
2	chr18:44332800-44334600	Weak transcription	Right Atrium	heart
3	chr18:44333600-44334600	Enhancers	Skeletal Muscle Female	skeletal muscle
4	chr18:44333600-44337400	Bivalent/Poised TSS	Fetal Brain Female	brain
5	chr18:44333800-44334600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
6	chr18:44333800-44334600	Bivalent Enhancer	Fetal Muscle Leg	muscle
7	chr18:44333800-44335800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
8	chr18:44334000-44334600	Flanking Active TSS	Brain Germinal Matrix	brain
9	chr18:44334000-44334600	Enhancers	Dnd41	blood
10	chr18:44334000-44335200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
11	chr18:44334000-44335800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
12	chr18:44334200-44334800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
13	chr18:44334200-44334800	Flanking Active TSS	GM12878-XiMat	blood
14	chr18:44334200-44334800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
15	chr18:44334200-44335000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
16	chr18:44334200-44335600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
17	chr18:44334200-44335800	Enhancers	Primary B cells from peripheral blood	blood
18	chr18:44334200-44336200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
19	chr18:44334200-44337800	Active TSS	Brain Angular Gyrus	brain
20	chr18:44334400-44334600	Flanking Active TSS	Brain Cingulate Gyrus	brain
21	chr18:44334400-44334600	Flanking Active TSS	Fetal Adrenal Gland	Adrenal Gland
22	chr18:44334400-44334800	Enhancers	Psoas Muscle	Psoas
23	chr18:44334400-44335200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
24	chr18:44334400-44335200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
25	chr18:44334400-44335800	Enhancers	Fetal Heart	heart
26	chr18:44334400-44335800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
27	chr18:44334400-44336400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
28	chr18:44334400-44338000	Active TSS	Brain Inferior Temporal Lobe	brain
29	chr18:44334400-44338400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain

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