Variant report

Variant	rs16940040
Chromosome Location	chr18:44334726-44334727
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

TF binding
region (count:1)
CpG islands
(count:61)
Chromatin interactive
region (count:0)
LncRNA
region (count:0)
Mature miRNA
region (count: 0)
miRNA target
sites (count:0)

(count:1 , 50 per page) page: 1

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr18:44334720-44334870	GM12872	blood:	n/a	chr18:44334781-44334794

(count:61 , 50 per page) page: 1 2

No.	Chromosome Location	Cell Line	Cell type	Cell Stage
1	chr18:44334713-44334763	HRE	kidney:	n/a
2	chr18:44334713-44334763	Hepatocyte	liver:	n/a
3	chr18:44334713-44334763	HRPEpiC	eye:	n/a
4	chr18:44334713-44334763	HNPCEpiC	eye:	n/a
5	chr18:44334713-44334763	HCPEpiC	choroid plexus:	n/a
6	chr18:44334713-44334763	HepG2	liver:	n/a
7	chr18:44334713-44334763	GM12892	blood:	n/a
8	chr18:44334713-44334763	HCM	heart:	n/a
9	chr18:44334713-44334763	SAEC	small airway:	n/a
10	chr18:44334713-44334763	PANC-1	pancreas:	n/a
11	chr18:44334713-44334763	Jurkat	blood:	n/a
12	chr18:44334713-44334763	SKMC	muscle:	n/a
13	chr18:44334713-44334763	U87	brain:	n/a
14	chr18:44334713-44334763	LNCaP	prostate:	n/a
15	chr18:44334713-44334763	CMK	blood:	n/a
16	chr18:44334713-44334763	HCT-116	colon:	n/a
17	chr18:44334713-44334763	HL-60	blood:	n/a
18	chr18:44334713-44334763	NHBE	bronchial:	n/a
19	chr18:44334713-44334763	AG09309	skin:	n/a
20	chr18:44334713-44334763	BE2_C	brain:	n/a
21	chr18:44334713-44334763	RPTEC	kidney:	n/a
22	chr18:44334713-44334763	HRCEpiC	kidney:	n/a
23	chr18:44334713-44334763	Hela-S3	cervix:	n/a
24	chr18:44334713-44334763	AoSMC	blood vessel:	n/a
25	chr18:44334713-44334763	K562	blood:	n/a
26	chr18:44334713-44334763	HUVEC	blood vessel:	n/a
27	chr18:44334713-44334763	GM12891	blood:	n/a
28	chr18:44334713-44334763	A549	lung:	n/a
29	chr18:44334713-44334763	AG04449	skin:	fetal
30	chr18:44334713-44334763	AG10803	skin:	n/a
31	chr18:44334713-44334763	HEEpiC	esophagus:	n/a
32	chr18:44334713-44334763	GM06990	blood:	n/a
33	chr18:44334713-44334763	AG09319	gingival:	n/a
34	chr18:44334713-44334763	SK-N-SH	brain:	n/a
35	chr18:44334713-44334763	PrEC	prostate:	n/a
36	chr18:44334713-44334763	NHDF-neo	bronchial:	n/a
37	chr18:44334713-44334763	HMEC	breast:	n/a
38	chr18:44334713-44334763	H1-hESC	embryonic stem cell:	embryo
39	chr18:44334713-44334763	HPAEpiC	pulmonary alveolar:	n/a
40	chr18:44334713-44334763	IMR90	lung:	fetal
41	chr18:44334713-44334763	GM19239	blood:	n/a
42	chr18:44334713-44334763	HAEpiC	amniotic membrane:	n/a
43	chr18:44334713-44334763	PFSK-1	brain:	n/a
44	chr18:44334713-44334763	AG04450	lung:	fetal
45	chr18:44334713-44334763	T-47D	breast:	n/a
46	chr18:44334713-44334763	ProgFib	skin:	n/a
47	chr18:44334713-44334763	HIPEpiC	eye:	n/a
48	chr18:44334713-44334763	Caco-2	colon:	n/a
49	chr18:44334713-44334763	NH-A	brain:	n/a
50	chr18:44334713-44334763	BJ	skin:	n/a

No data

Variant related genes	Relation type
ENSG00000270112	TF binding region
ENSG00000270112	CpG island

Extended variants
information (count: 30 )
Associated
traits (count: 5 )

rSNPs within LD-proxies of this variant (count:12)

rs_ID	r²[population]
rs11082558	0.83[ASN][1000 genomes]
rs12454436	1.00[CEU][hapmap];1.00[CHB][hapmap];1.00[JPT][hapmap];1.00[AMR][1000 genomes];1.00[EUR][1000 genomes];1.00[ASN][1000 genomes]
rs16940043	0.86[ASN][1000 genomes]
rs2298778	0.84[JPT][hapmap]
rs3809962	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.96[ASN][1000 genomes]
rs3893181	0.86[CHD][hapmap];0.89[JPT][hapmap];0.83[ASN][1000 genomes]
rs4121691	0.85[ASN][1000 genomes]
rs4449041	0.94[CHB][hapmap];1.00[CHD][hapmap];1.00[GIH][hapmap];1.00[JPT][hapmap];0.95[ASN][1000 genomes]
rs59166390	0.82[ASN][1000 genomes]
rs7237805	0.84[JPT][hapmap]
rs73434915	0.92[ASN][1000 genomes]
rs8085861	0.80[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:5)

SNP	Gene	Cis/trans	Tissue	Source
rs16940040	ST8SIA5	cis	lymphoblastoid	seeQTL
rs16940040	SIGLEC15	cis	parietal	SCAN
rs16940040	IER3IP1	cis	cerebellum	SCAN
rs16940040	ATP5A1	cis	parietal	SCAN
rs16940040	SLC14A1	cis	parietal	SCAN

Chromatin state (count:34 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr18:44332600-44335000	Weak transcription	HSMMtube	muscle
2	chr18:44333600-44337400	Bivalent/Poised TSS	Fetal Brain Female	brain
3	chr18:44333800-44335800	Bivalent Enhancer	iPS-18 Cell Line	embryonic stem cell
4	chr18:44334000-44335200	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Male	--
5	chr18:44334000-44335800	Enhancers	ES-UCSF4 Cell Line	embryonic stem cell
6	chr18:44334200-44334800	Enhancers	Primary Natural Killer cells fromperipheralblood	blood
7	chr18:44334200-44334800	Flanking Active TSS	GM12878-XiMat	blood
8	chr18:44334200-44334800	Flanking Active TSS	Monocytes-CD14+_RO01746	blood
9	chr18:44334200-44335000	Weak transcription	iPS DF 6.9 Cell Line	embryonic stem cell
10	chr18:44334200-44335600	Bivalent Enhancer	Primary hematopoietic stem cells G-CSF-mobilized Female	--
11	chr18:44334200-44335800	Enhancers	Primary B cells from peripheral blood	blood
12	chr18:44334200-44336200	Bivalent Enhancer	Primary monocytes fromperipheralblood	blood
13	chr18:44334200-44337800	Active TSS	Brain Angular Gyrus	brain
14	chr18:44334400-44334800	Enhancers	Psoas Muscle	Psoas
15	chr18:44334400-44335200	Active TSS	Ganglion Eminence derived primary cultured neurospheres	brain
16	chr18:44334400-44335200	Bivalent Enhancer	Fetal Muscle Trunk	muscle
17	chr18:44334400-44335800	Enhancers	Fetal Heart	heart
18	chr18:44334400-44335800	Flanking Active TSS	Skeletal Muscle Male	skeletal muscle
19	chr18:44334400-44336400	Bivalent Enhancer	Primary hematopoietic stem cells short term culture	blood
20	chr18:44334400-44338000	Active TSS	Brain Inferior Temporal Lobe	brain
21	chr18:44334400-44338400	Active TSS	Brain Dorsolateral Prefrontal Cortex	brain
22	chr18:44334600-44334800	Bivalent Enhancer	Primary T helper cells fromperipheralblood	blood
23	chr18:44334600-44334800	Flanking Bivalent TSS/Enh	Fetal Muscle Leg	muscle
24	chr18:44334600-44335000	Enhancers	iPS DF 19.11 Cell Line	embryonic stem cell
25	chr18:44334600-44335000	Flanking Active TSS	Cortex derived primary cultured neurospheres	brain
26	chr18:44334600-44335000	Enhancers	Right Atrium	heart
27	chr18:44334600-44335200	Enhancers	H1 Cell Line	embryonic stem cell
28	chr18:44334600-44335200	Active TSS	Brain Cingulate Gyrus	brain
29	chr18:44334600-44335400	Bivalent Enhancer	HUES6 Cell Line	embryonic stem cell
30	chr18:44334600-44335400	Bivalent Enhancer	iPS-15b Cell Line	embryonic stem cell
31	chr18:44334600-44335600	Flanking Bivalent TSS/Enh	Fetal Adrenal Gland	Adrenal Gland
32	chr18:44334600-44335800	Flanking Active TSS	Skeletal Muscle Female	skeletal muscle
33	chr18:44334600-44336000	Active TSS	Brain Germinal Matrix	brain
34	chr18:44334600-44336200	Enhancers	Spleen	Spleen

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